From 9f672d2f0ed66826cbd25d3a249818237bc15d83 Mon Sep 17 00:00:00 2001 From: Alexander Sullivan Date: Wed, 18 Feb 2026 13:16:53 -0500 Subject: [PATCH 1/3] update packages --- EDIT.MD | 14 +- README.md | 2 +- core/scripts/crispr_scripts.js | 77 +- core/scripts/crispr_scripts.test.js | 5 - core/scripts/login.js | 22 +- core/scripts/login.test.js | 5 - core/systemrun.html | 2 +- docs/api/index.md | 162 +--- docs/architecture/index.md | 193 ++-- docs/guides/data-structures.md | 265 +++--- docs/guides/marking-algorithm.md | 258 ++---- docs/guides/setup.md | 96 +- docs/index.md | 97 +- package-lock.json | 1322 ++++++++++++--------------- package.json | 12 +- 15 files changed, 1106 insertions(+), 1426 deletions(-) diff --git a/EDIT.MD b/EDIT.MD index f5d8188..8aa0c32 100644 --- a/EDIT.MD +++ b/EDIT.MD @@ -16,11 +16,11 @@ There is also a feedback page for practice assignments screen which is displayed ## Example protocol -There is an example protocol for students to follow in the PDF file [LabProtocol](LabProtocol.pdf). It is recommended that you customize it to your teaching class, but the protocol includes all the necessary details for students to follow to understand how to create gRNAs and where they can get the information to input into SciGrade. +There is an example protocol for students to follow in [LabProtocol.pdf](LabProtocol.pdf). It is recommended that you customize it to your teaching class, but the protocol includes details for students to follow to understand how to create guide RNAs (gRNAs) and where they can get the information to input into SciGrade. ## Marking algorithm -SciGrade marks the gRNA strand, PAM sequence, off-target score and the F1 and R1 primers. Using [markAnswers()](core/scripts/crispr_scripts.js), the student's input into the form will be used to determine the marking. +SciGrade validates the gRNA strand, Protospacer Adjacent Motif (PAM) sequence, off-target score, and the F1/R1 primers, and it scores gRNA sequence, PAM, off-target, and primer inputs in [markAnswers()](core/scripts/crispr_scripts.js). The marking algorithm is fully contained in the client-side code and uses the reference data from [Benchling_gRNA_Outputs.json](core/data/Benchling_gRNA_Outputs.json) to validate answers. @@ -32,7 +32,7 @@ Regarding the algorithm, student marks are dependent on 5 inputs: 4. F1 primer 5. R1 primer. -The cut site is used to calculate whether the students have put in a valid gRNA sequence and its corresponding inputs. If the gRNA sequence is not found within a set range the [Benchling gRNA Output results](core/data/Benchling_gRNA_Outputs.json), then it is not a valid gRNA. If the gRNA sequence is not valid, all their answers would be wrong. +The cut site is used to calculate whether the student-selected gRNA sequence includes the target position and satisfies the range checks in [core/scripts/crispr_scripts.js](core/scripts/crispr_scripts.js). If the gRNA sequence does not match a reference sequence in [core/data/Benchling_gRNA_Outputs.json](core/data/Benchling_gRNA_Outputs.json), the remaining validation steps are skipped. The following image describes where student's marks come from in the marking algorithm. @@ -48,7 +48,7 @@ Edit the code within [crispr_scripts.js](core/scripts/crispr_scripts.js). The fo - `checkR1Primers(seq)` - Validates reverse primers - `markAnswers()` - Assigns scores based on validation results -For off-target score thresholds, the optimal value is calculated using: `Min_optimal = Max_range - (Max_range * 0.2)` where `Max_range` is the highest possible off-target score for a gene. You can adjust this calculation or implement custom logic in the `checkOffTarget()` function. +For off-target score thresholds, the optimal value is calculated using `Min_optimal = Max_range - (Max_range * 0.2)` and the threshold is set to 80 when `Min_optimal` is greater than 80 or less than 35 in [checkOffTarget()](core/scripts/crispr_scripts.js). ## Adding new genes @@ -90,3 +90,9 @@ If you have any questions or would like to get in contact with the maintainers, Enjoy! :relaxed: :heart: -[Alex](https://twitter.com/alexjsully) + +## Related Documentation + +- [docs/index.md](docs/index.md) - Documentation entry point +- [docs/guides/marking-algorithm.md](docs/guides/marking-algorithm.md) - Marking flow details +- [docs/guides/data-structures.md](docs/guides/data-structures.md) - JSON reference data diff --git a/README.md b/README.md index da060a2..3e687eb 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ SciGrade is an online web-tool that allows students (or any user with access) to ## Getting Started -It is recommended that you use the web-version available at but if you want to download and run the SciGrade locally, it is possible though it requires an internet connection to login and accesses the marking form and student information (exclusive for TA's and admins). +It is recommended that you use the web-version available at . For local runs, the landing page [index.html](index.html) links to the runtime page [core/systemrun.html](core/systemrun.html), which initializes the practice flow by default and hides the account UI in the navigation. ## Browser Compatibilities diff --git a/core/scripts/crispr_scripts.js b/core/scripts/crispr_scripts.js index 28bb298..788a38f 100644 --- a/core/scripts/crispr_scripts.js +++ b/core/scripts/crispr_scripts.js @@ -11,9 +11,7 @@ const listOfGenes = ["eBFP", "ACTN3", "HBB", "CCR5", "ANKK1", "APOE"]; let possible_gene = "eBFP"; let current_gene = "empty"; -/** - * Purpose of this is to assign the current gene and check for errors - */ +/** Purpose of this is to assign the current gene and check for errors */ function select_Gene() { if (possible_gene !== "" || possible_gene) { current_gene = possible_gene; @@ -198,9 +196,9 @@ function loadWork() { } /** - * @param {event} evt - Character key press - * @return {bool} - Returns true if number or dash, else false - * Determine if a number or dash key is pressed + * Determine if a number, dash, or period key is pressed. + * @param {Event} evt - Character key press event + * @returns {boolean} True if the key is a number, dash, or period */ function isNumberOrDashKey(evt) { const charCode = evt.which ? evt.which : evt.keyCode; @@ -384,7 +382,7 @@ function checkAnswers() { // Check if the F1 primer matches the answer's input checkF1Primers(document?.getElementById("sequence_input")?.value?.trim() || ""); - // Check if the F1 primer matches the answer's input + // Check if the R1 primer matches the answer's input checkR1Primers(document?.getElementById("sequence_input")?.value?.trim() || ""); } } @@ -398,9 +396,8 @@ let offtarget_dict = {}; let offtarget_dictParse = []; let offtarget_Use = []; /** - * Checks the off-target score if it is correct - * @param {int} score - The specificity score from possible_comparable_answers - * @return {bool} - Returns true if MAROffTarget is correct + * Checks whether the submitted off-target score matches the reference scoring rules. + * @param {number} score - Reference specificity score from the matched gRNA entry */ function checkOffTarget(score) { // Reset variables: @@ -481,9 +478,8 @@ function checkOffTarget(score) { let possible_F1_primers = []; /** - * Checks if the F1 primer is correct or not - * @param {String} seq - The gRNA sequence - * @return {bool} - Returns true if MARF1primers is correct + * Checks whether the F1 primer matches one of the generated candidates. + * @param {string} seq - The gRNA sequence */ function checkF1Primers(seq) { // Reset variables: @@ -516,9 +512,8 @@ const complementary_nt_dict = { G: "C", }; /** - * Checks if the R1 primer is correct or not - * @param {String} seq - The gRNA sequence - * @return {bool} - Returns true if MARR1primers is correct + * Checks whether the R1 primer matches one of the generated candidates. + * @param {string} seq - The gRNA sequence */ function checkR1Primers(seq) { // Reset variables: @@ -539,7 +534,8 @@ function checkR1Primers(seq) { } /** - * Creates a complementary sequence of the nucleotides + * Builds a complementary sequence from the provided nucleotides. + * Note: This function does not return the computed sequence. */ function createComplementarySeq(seq) { let comp_seq = ""; @@ -551,8 +547,9 @@ function createComplementarySeq(seq) { let studentMark = 0; let studentMarkPercentage = 0; const markTotal = 10; + /** - * Based on checkAnswers(), returns a float of a mark + * Calculates the student's mark and percentage based on the current marking state. */ function markAnswers() { studentMark = 0; @@ -806,9 +803,9 @@ function showFeedback() { /** * Determine whether an input form will be displayed or not - * @param {String} docCheck The DOM being checked against - * @param {String} checkFor The value of the DOM being used to check for - * @param {String} docDisplay The DOM what will toggle hidden visibility for + * @param {string} docCheck The DOM being checked against + * @param {string} checkFor The value of the DOM being used to check for + * @param {string} docDisplay The DOM what will toggle hidden visibility for */ function showNewInput(docCheck, checkFor, docDisplay) { if (document.getElementById(String(docCheck)).value === String(checkFor)) { @@ -1206,7 +1203,7 @@ function openAccountManagement() { /** * Update the choose user's options in the account management's change user type - * @param {String} domUser + * @param {string} domUser */ function UpdateChooseUser(domUser) { ClearSelectOptions(domUser); @@ -1219,9 +1216,9 @@ function UpdateChooseUser(domUser) { /** * Add more options to a select - * @param {String} domID The DOM ID in the HTML file for the select - * @param {String} optionsValue The value and ID for the options being added - * @param {String} optionsInner The InnerHTML for the options being added + * @param {string} domID The DOM ID in the HTML file for the select + * @param {string} optionsValue The value and ID for the options being added + * @param {string} optionsInner The InnerHTML for the options being added */ function AddToOptions(domID, optionsValue, optionsInner) { const dom = document.getElementById(domID); @@ -1233,7 +1230,7 @@ function AddToOptions(domID, optionsValue, optionsInner) { /** * Clear an select's options - * @param {String} domID The DOM ID in the HTML for the select + * @param {string} domID The DOM ID in the HTML for the select */ function ClearSelectOptions(domID) { const dom = document.getElementById(domID); @@ -1245,7 +1242,7 @@ function ClearSelectOptions(domID) { let updatedListOfStudents = {}; /** * Update the list of students available for a class - * @param {String} className The class for which the students belong to + * @param {string} className The class for which the students belong to */ function UpdateStudentList(className) { updatedListOfStudents = {}; @@ -1259,8 +1256,8 @@ function UpdateStudentList(className) { /** * Change a DOM's innerHTML - * @param {String} domID DOM's ID that is being modified - * @param {String} changeTo The content of the innerHTML + * @param {string} domID DOM's ID that is being modified + * @param {string} changeTo The content of the innerHTML */ function ChangeDOMInnerhtml(domID, changeTo) { document.getElementById(domID).innerHTML = changeTo; @@ -1270,9 +1267,9 @@ const downloadIndexTable_start = "\t\t\n\t\t\tStudent Number\n\t\t\ const downloadIndexTable_end = "\n\t\t\n"; let downloadIndexTable_fill = ""; /** - * Generated the base IndexTable for downloading JSON as CSV - * @param {String} whichIndexTable The string of which the index table start as, defaults as downloadIndexTable_start - * @param {boolean} SimpleComplex True is simple, false is complex + * Generates the base index table header used for CSV export. + * @param {string} whichIndexTable Placeholder parameter for compatibility + * @param {boolean} SimpleComplex Placeholder parameter for compatibility */ function generateRestOfIndexTable(whichIndexTable, SimpleComplex) { whichIndexTable = downloadIndexTable_start; @@ -1282,7 +1279,7 @@ function generateRestOfIndexTable(whichIndexTable, SimpleComplex) { /** * Generated a download button from JSON to CSV - * @param {String} whichClass Which class is being downloaded + * @param {string} whichClass Which class is being downloaded * @param {boolean} whichType True is simple, false is complex */ function generateHiddenStudentDownload(whichClass, whichType) { @@ -1322,11 +1319,11 @@ function generateHiddenStudentDownload(whichClass, whichType) { } /** - * Changes the input class value to new input - * @param {String} docCheck The DOM being checked against - * @param {String} checkFor The value of the DOM being used to check for - * @param {String} docChange The DOM what will have its value changed - * @param {String} trueChangeValueTo What to change value to + * Updates one input value when another input matches a target value. + * @param {string} docCheck The DOM ID to check + * @param {string} checkFor The value to compare against + * @param {string} docChange The DOM ID to update + * @param {string} trueChangeValueTo The value to apply when matched */ function changeInputClass(docCheck, checkFor, docChange, trueChangeValueTo) { if (trueChangeValueTo === "" || trueChangeValueTo === undefined) { @@ -1345,7 +1342,7 @@ let studentAnswers = `student_list.${studentParseNum}.${loadedMode}-${current_ge let studentOutputs = `student_list.${studentParseNum}.${loadedMode}-${current_gene}-Outputs`; let studentMarks = `student_list.${studentParseNum}.${loadedMode}-${current_gene}-Marks`; /** - * Submit and sends the student's answers to the server + * Collects the student's answers, calculates marks, and triggers feedback display. */ function submitAnswers() { all_answers = []; @@ -1395,7 +1392,7 @@ function submitAnswers() { /** * Determine if a enter was pressed and if so, click a button * @param {Event} event The key press - * @param {String} toClickButton Which button to click + * @param {string} toClickButton Which button to click */ function IfPressEnter(event, toClickButton) { if (event.which === 13 || event.keyCode === 13) { diff --git a/core/scripts/crispr_scripts.test.js b/core/scripts/crispr_scripts.test.js index b9a4cb3..c564314 100644 --- a/core/scripts/crispr_scripts.test.js +++ b/core/scripts/crispr_scripts.test.js @@ -1,8 +1,3 @@ -/** - * Unit tests for crispr_scripts.js - * Tests isolated utility functions and logic - */ - describe("crispr_scripts.js - Utility Functions", () => { // Test the isNumberOrDashKey function without DOM dependencies describe("isNumberOrDashKey()", () => { diff --git a/core/scripts/login.js b/core/scripts/login.js index e3d5638..be716f9 100644 --- a/core/scripts/login.js +++ b/core/scripts/login.js @@ -6,7 +6,7 @@ let student_reg_information; -/** Let users continue with practice application without logging in (true) (default false) */ +/** Let users continue with practice application without logging in (default true) */ let continueWithoutLogin = true; let checkStudentNum = false; @@ -14,13 +14,12 @@ let studentNumber = 0; let studentUmail; let alreadyRegistered = false; let classRegister; + /** - * Check to determine if the student is within - * @param {Num} student_num Student number - * @param {String} student_umail Student's email/uMail - * @return {bool} checkStudentNum - Whether the student is a student in the system or not + * Checks whether a student number and email match the class roster. + * @param {number} student_num Student number + * @param {string} student_umail Student email/uMail */ - function checkStudentNumber(student_num, student_umail) { alreadyRegistered = false; checkStudentNum = false; @@ -67,8 +66,8 @@ function checkStudentNumber(student_num, student_umail) { } /** - * Check to determine if the student is registered in the system - * @param {Num} student_num - Student number + * Checks whether a student number exists in the registration list. + * @param {number} student_NumVerify - Student number */ function loginVerify(student_NumVerify) { alreadyRegistered = false; @@ -103,8 +102,8 @@ function loginVerify(student_NumVerify) { } /** - * Which reg error shows - * @param {Num} whichOne - Number indicator for which error to show + * Shows a registration error message by code. + * @param {number} whichOne - Error code to display */ function showRegError(whichOne) { if (whichOne === 1) { @@ -201,8 +200,9 @@ function loadGeneContent() { } const changeLogin = ''; + /** - * Once users have registered OR logged in, the page dynamically generates the CRISPR assignment page + * Builds the selection UI and loads the reference data for the runtime page. */ async function redirectCRISPR() { $("#mainContainer").empty(); diff --git a/core/scripts/login.test.js b/core/scripts/login.test.js index ac92cf1..0c7a11a 100644 --- a/core/scripts/login.test.js +++ b/core/scripts/login.test.js @@ -1,8 +1,3 @@ -/** - * Unit tests for login.js - * Tests isolated utility functions and logic - */ - describe("login.js - Utility Functions", () => { // Test the checkStudentNumber function logic describe("checkStudentNumber()", () => { diff --git a/core/systemrun.html b/core/systemrun.html index d96f209..bcdc650 100644 --- a/core/systemrun.html +++ b/core/systemrun.html @@ -134,7 +134,7 @@ /** * Handle changing navigation tabs between login and register - * @param {String} [which='login'] Which tab is being switched to (default login) + * @param {string} [which='login'] Which tab is being switched to (default login) * @example Use this function to handle switching between the login and register content * handleLoginTabChange('login') * // returns null (does not return anything but rather un-hides the login content) diff --git a/docs/api/index.md b/docs/api/index.md index a97638c..f2d9b80 100644 --- a/docs/api/index.md +++ b/docs/api/index.md @@ -10,7 +10,7 @@ This document provides detailed function signatures and descriptions for the cor **Location:** [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) -Core application logic for gRNA sequence validation, marking, and feedback generation. +Core application logic for guide RNA (gRNA) sequence validation, marking, and feedback generation. ### Global Variables @@ -27,7 +27,7 @@ let benchling_gRNA_outputs; // Loaded gRNA validation data // Marking state let MARgRNAseq; // gRNA sequence validation result let MARgRNAseq_degree; // gRNA validation degree (0-3) -let MARPAMseq; // PAM sequence validation result +let MARPAMseq; // Protospacer Adjacent Motif (PAM) sequence validation result let MARCutPos; // Cut position validation result let MARstrand; // Strand selection validation result let MAROffTarget; // Off-target score validation result @@ -83,7 +83,7 @@ async function loadCRISPRJSON_Files() **Returns:** Promise (implicitly handled by async). -**Called By:** Application initialization in [index.html](../../index.html). +**Called By:** `redirectCRISPR()` in [core/scripts/login.js](../../core/scripts/login.js), which is triggered on page load from [core/systemrun.html](../../core/systemrun.html). **Example:** @@ -136,10 +136,10 @@ function loadWork() - Clears the `#work` HTML element - Sets `loadedMode` to `selection_inMode` - Generates form HTML including: - - Gene background information section - - Input fields for gRNA sequence, PAM, strand, position, off-target score - - Input fields for F1 and R1 primers - - Submit button with `submitAnswers()` handler + - Gene background information section + - Input fields for gRNA sequence, PAM, strand, position, off-target score + - Input fields for F1 and R1 primers + - Submit button with `submitAnswers()` handler **Renders to:** HTML element with ID `work`. @@ -194,7 +194,7 @@ function checkAnswers() 1. Resets all marking variables 2. Retrieves student input from form fields -3. Searches for matching gRNA sequences in reference data +3. Searches for matching gRNA sequences in reference data with an exact, case-sensitive match after trimming 4. For each match: - Validates strand selection - Checks if target nucleotide is in range @@ -225,13 +225,14 @@ function checkOffTarget(score) **Behavior:** -- Compares score against optimal threshold -- Sets `MAROffTarget` and `MAROffTarget_degree` variables +- Compares the student input to the floor/ceiling of the reference specificity score +- Builds a score list within ±35 positions of the inputted cut position to determine an optimal threshold +- Sets `MAROffTarget` and `MAROffTarget_degree` based on the input and calculated thresholds - Degree values: - - `0`: Wrong (score too low) - - `1`: Above optimal threshold - - `2`: Above 35 (minimum viable) - - `3`: Only available option + - `0`: Wrong or below threshold + - `1`: At or above the optimal threshold + - `2`: At or above 35 but below the optimal threshold when the max reference score is at least 80 + - `3`: Only available option when the local max score is below 35 **Used For:** Part of `checkAnswers()` validation. @@ -249,8 +250,9 @@ function checkF1Primers(seq) **Behavior:** -- Checks if F1 primer contains required promoter and binding sequences -- Validates structure against expected format +- Builds candidate F1 primers using the `TAATACGACTCACTATAG` prefix and the first 16-20 bases of the input gRNA +- If the gRNA starts with `G`, also builds candidates using bases 2-20 +- Sets `MARF1primers` when the submitted F1 primer matches a candidate **Sets:** `MARF1primers` global variable. @@ -275,43 +277,14 @@ function checkR1Primers(seq) **Behavior:** -- Generates reverse complement of gRNA sequence -- Checks if R1 primer contains the reverse complement +- Generates a reverse-complement string using the `complementary_nt_dict` mapping +- Builds candidate R1 primers using the `TTCTAGCTCTAAAAC` prefix and the first 19-20 bases of the reverse complement +- Sets `MARR1primers` when the submitted R1 primer matches a candidate **Sets:** `MARR1primers` global variable. **Depends On:** Valid gRNA sequence already validated. -#### createComplementarySeq(seq) - -```javascript -function createComplementarySeq(seq) -returns {string} -``` - -**Purpose:** Create the reverse complement of a DNA sequence. - -**Parameters:** - -- `seq` {string} - DNA sequence (ACGT) - -**Process:** - -1. Replace each base with complement: A↔T, G↔C -2. Reverse the string - -**Returns:** Reverse complement sequence. - -**Example:** - -```javascript -const complement = createComplementarySeq("ACGT"); -console.log(complement); // "ACGT" (palindromic) - -const complement2 = createComplementarySeq("AAAA"); -console.log(complement2); // "TTTT" -``` - ### Marking & Feedback #### markAnswers() @@ -326,12 +299,12 @@ function markAnswers() - Processes results from `checkAnswers()` - Assigns points for each correct component: - - gRNA sequence - - PAM - - Strand - - Off-target score - - F1 primer - - R1 primer + - gRNA sequence + - PAM + - Strand + - Off-target score + - F1 primer + - R1 primer - Calculates weighted final score **Prerequisite:** `checkAnswers()` must be called first. @@ -351,18 +324,10 @@ function showFeedback() **Renders:** - Component-by-component results (✓ or ✗) -- Correct answers if student answer was wrong -- Explanation of off-target scoring -- Primer design guidance +- Explanatory text derived from the current marking state +- Candidate primer lists derived from the submitted gRNA sequence -**Rendered To:** Feedback section in HTML. - -**Shows:** - -- Correct gRNA sequence (if student's was wrong) -- Correct PAM (if student's was wrong) -- Optimal off-target threshold -- Overall score and performance +**Rendered To:** `#mainContainer` in the runtime page. **Called By:** `submitAnswers()` after `markAnswers()`. @@ -378,11 +343,9 @@ function submitAnswers() **Workflow:** -1. Validate form inputs -2. Call `checkAnswers()` for validation -3. Call `markAnswers()` for scoring -4. Call `showFeedback()` to display results -5. Store submission in browser (if applicable) +1. Call `checkAnswers()` for validation +2. After a delay, call `markAnswers()` for scoring +3. Call `showFeedback()` to display results **Form Elements Referenced:** @@ -402,11 +365,11 @@ function submitAnswers() function IfPressEnter(event, toClickButton) ``` -**Purpose:** Trigger action when Enter key is pressed (accessibility). +**Purpose:** Trigger action when Enter key is pressed. **Parameters:** -- `event` {event} - Keyboard event +- `event` {Event} - Keyboard event - `toClickButton` {string} - Button ID to trigger **Behavior:** Simulates click on specified button if Enter key pressed. @@ -417,20 +380,6 @@ function IfPressEnter(event, toClickButton) ``` -### Account Management (Deprecated) - -#### openAccountManagement() ⚠️ DEPRECATED - -```javascript -function openAccountManagement() -``` - -**Status:** Deprecated in v1.2.0. This function is no longer used. - -**Legacy Purpose:** Displayed account management modal (TA/Admin feature - no longer available). - -**Note:** Authentication features were deprecated with the May 2, 2024 v1.2.0 release. See [CHANGELOG.md](../../CHANGELOG.md) for details. - ### Display Functions #### showNewInput(docCheck, checkFor, docDisplay) @@ -447,7 +396,7 @@ function showNewInput(docCheck, checkFor, docDisplay) - `checkFor` {string} - Value to check for - `docDisplay` {string} - Element ID to display/hide -**Behavior:** Shows `docDisplay` if `docCheck` contains `checkFor`. +**Behavior:** Shows `docDisplay` when `docCheck` matches `checkFor`. #### ChangeDOMInnerhtml(domID, changeTo) @@ -468,41 +417,26 @@ function ChangeDOMInnerhtml(domID, changeTo) function changeInputClass(docCheck, checkFor, docChange, trueChangeValueTo) ``` -**Purpose:** Toggle CSS classes on elements for visual feedback. +**Purpose:** Update an input value when another input matches a target value. **Parameters:** - `docCheck` {string} - Element ID to check condition - `checkFor` {string} - Value to match -- `docChange` {string} - Element ID to change class on -- `trueChangeValueTo` {string} - CSS class to apply - -## Deprecated: login.js (v1.2.0+) - -**Location:** [core/scripts/login.js](../../core/scripts/login.js) - -**Status:** Deprecated in v1.2.0 (May 2, 2024). All authentication and account management features are no longer available. - -The following functions are preserved for historical reference only: - -- `checkStudentNumber()` - Student credential validation (deprecated) -- `openAccountManagement()` - Account management interface (deprecated) -- `UpdateChooseUser()` - User context switching (deprecated) -- `UpdateStudentList()` - Class roster management (deprecated) - -These functions are not used in the current version. Online features including multi-user authentication, class management, and database integration were removed in v1.2.0. See [CHANGELOG.md](../../CHANGELOG.md) for full deprecation details. +- `docChange` {string} - Element ID to update +- `trueChangeValueTo` {string} - Value to apply when matched ## Bootstrap & jQuery ### Bootstrap Classes -The application uses Bootstrap utilities for styling: +The application uses Bootstrap utilities for styling in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) and [core/systemrun.html](../../core/systemrun.html): ```html
- - + +
@@ -511,9 +445,9 @@ The application uses Bootstrap utilities for styling:
-
-
-
+
+
+
``` @@ -535,6 +469,8 @@ const element = document.getElementById("sequence_input"); ## Error Codes +Error codes are raised by alerts in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). + | Code | Context | Meaning | | -------- | ------------- | --------------------- | | sG34-42 | select_Gene() | Gene selection failed | @@ -552,6 +488,6 @@ npm run test:jest ## Related Documentation -- [Marking Algorithm](marking-algorithm.md) - Detailed validation logic -- [Data Structures](data-structures.md) - JSON format specifications +- [Marking Algorithm](../guides/marking-algorithm.md) - Detailed validation logic +- [Data Structures](../guides/data-structures.md) - JSON format specifications - [Architecture](../architecture/index.md) - System design overview diff --git a/docs/architecture/index.md b/docs/architecture/index.md index 2b28585..1fcb2b8 100644 --- a/docs/architecture/index.md +++ b/docs/architecture/index.md @@ -1,19 +1,19 @@ # Architecture -SciGrade is a client-side web application that dynamically renders the gRNA and primer validation interface. This section covers the system design, data flow, and component relationships. +SciGrade is a client-side web application that dynamically renders the guide RNA (gRNA) and primer validation interface. This section covers the system design, data flow, and component relationships. + +The landing page is [index.html](../../index.html), and the runtime page is [core/systemrun.html](../../core/systemrun.html). The runtime page loads the client scripts and initializes the UI flow defined in [core/scripts/login.js](../../core/scripts/login.js) and [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ## System Overview ```mermaid graph TD A[Browser/Client] -->|HTTP Requests| B[Static Web Server] - A -->|Load Scripts| C[crispr_scripts.js] - A -->|Load Scripts| D[login.js] - C -->|Fetch JSON| E["Gene Data
(Benchling_gRNA_Outputs.json)"] - C -->|Fetch JSON| F["Gene Info
(gene_background_info.json)"] - C -->|Call Functions| G[Marking Algorithm] - D -->|Manage| H[User Sessions
Legacy Code] - G -->|Store Results| I["Browser LocalStorage
Session Data"] + B --> C[Landing Page] + C --> D[App Runtime Page] + D --> E[Client Scripts] + E --> F[JSON Data Files] + E --> G[Marking and Feedback UI] ``` ## Core Components @@ -28,29 +28,30 @@ Main application logic for gRNA and primer validation. - `loadCRISPRJSON_Files()` - Load gene data and benchling outputs asynchronously - `fillGeneList()` - Populate gene selection dropdown -- `loadWork()` - Dynamically render the assignment form +- `loadWork()` - Dynamically render the input form - `checkAnswers()` - Validate student input against reference data - `markAnswers()` - Calculate scores based on validation results - `submitAnswers()` - Handle form submission **Global State:** -- `selection_inMode` - Current mode ("practice" or "assignment") +- `selection_inMode` - Current mode string (defaults to "practice") - `current_gene` - Currently selected gene - `gene_backgroundInfo` - Loaded gene reference data - `benchling_gRNA_outputs` - Loaded gRNA validation reference #### [core/scripts/login.js](../../core/scripts/login.js) -Legacy code for user management (authentication features deprecated in v1.2.0). +UI bootstrap and account-management helpers used by the runtime page. **Key Functions:** -- `checkStudentNumber()` - Legacy student credential validation -- `openAccountManagement()` - Legacy account modal (deprecated) -- `UpdateChooseUser()` - Legacy user switching (deprecated) +- `redirectCRISPR()` - Builds the selection UI and triggers data loading +- `loadGeneContent()` - Reads the selected gene and calls `select_Gene()` +- `checkStudentNumber()` - Validates class membership against `student_reg_information` +- `loginVerify()` - Checks a student record for registration status -**Note:** These features are no longer used in the default configuration. See [CHANGELOG.md](../../CHANGELOG.md) for deprecation details. +**Note:** The default runtime flow hides the account UI and initializes the practice flow on page load in [core/systemrun.html](../../core/systemrun.html). The deprecation of online account features is recorded in [CHANGELOG.md](../../CHANGELOG.md). ### Data Files @@ -62,18 +63,18 @@ Structure: ```json { - "gene_list": { - "GENENAME": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] - } + "gene_list": { + "GENENAME": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] + } } ``` @@ -85,17 +86,17 @@ Structure: ```json { - "gene_list": { - "GENENAME": { - "base_type": "practice", - "name": "Gene Full Name", - "Background": "Educational description...", - "Target site": "Nucleotide position X - target description", - "Target position": "123", - "Sequence": "ACGT...", - "NCBI gene link": "https://..." - } - } + "gene_list": { + "GENENAME": { + "base_type": "practice", + "name": "Gene Full Name", + "Background": "Educational description...", + "Target site": "Nucleotide position X - target description", + "Target position": "123", + "Sequence": "ACGT...", + "NCBI gene link": "https://..." + } + } } ``` @@ -124,89 +125,93 @@ Built with Bootstrap utilities integrated via [core/scripts/APIandLibraries/Boot ### Initialization Flow +The initialization flow is driven by [index.html](../../index.html), [core/systemrun.html](../../core/systemrun.html), [core/scripts/login.js](../../core/scripts/login.js), and [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). + ```mermaid sequenceDiagram - Browser->>index.html: Load page - index.html->>crispr_scripts.js: Parse script - index.html->>login.js: Parse script - crispr_scripts.js->>loadCRISPRJSON_Files: Execute on load - loadCRISPRJSON_Files->>Benchling_gRNA_Outputs.json: Fetch - loadCRISPRJSON_Files->>gene_background_info.json: Fetch - crispr_scripts.js->>fillGeneList: Populate dropdown - login.js->>checkStudentNumber: Validate user if needed + Browser->>LandingPage: Load landing page + Browser->>RuntimePage: Navigate to app page + RuntimePage->>UI: Load scripts + UI->>UI: Build selection UI + UI->>Data: Fetch gene data + Data-->>UI: Return data + UI->>UI: Populate gene dropdown ``` -### Assignment Workflow +### Submission Workflow + +Submission flow is implemented in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ```mermaid sequenceDiagram Student->>UI: Select gene - UI->>loadWork: Render assignment form + UI->>loadWork: Render input form Student->>UI: Enter gRNA + primers Student->>UI: Click Submit - UI->>submitAnswers: Validate form + UI->>submitAnswers: Trigger submission flow submitAnswers->>checkAnswers: Check all fields - checkAnswers->>Benchling_gRNA_Outputs.json: Compare gRNA - checkAnswers->>gene_background_info.json: Get target position - checkAnswers->>Marking Algorithm: Calculate score - Marking Algorithm->>Student: Show feedback/results + checkAnswers->>Data: Compare gRNA and target position + submitAnswers->>markAnswers: Calculate score + submitAnswers->>showFeedback: Render feedback UI + showFeedback->>Student: Display feedback ``` ### Marking Process +Marking is driven by `checkAnswers()`, `checkOffTarget()`, and `markAnswers()` in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). + ```mermaid flowchart TD - A[Student Submission] --> B{gRNA Sequence
in Reference?} - B -->|No| C[All Answers Wrong] - B -->|Yes| D{Correct
Strand?} + A[Student Submission] --> B{gRNA Sequence Match?} + B -->|No| C[No gRNA Credit] + B -->|Yes| D{Strand and Target Range Valid?} D -->|No| C - D -->|Yes| E{Off-target
Score Valid?} - E -->|No| C - E -->|Yes| F{F1/R1
Primers Valid?} - F -->|No| G[Partial Credit] - F -->|Yes| H[Full Credit] - C --> I[Final Score & Feedback] - G --> I - H --> I + D -->|Yes| E{PAM Match?} + E -->|No| F[Partial Credit Path] + E -->|Yes| G{Off-target Score Valid?} + G -->|No| F + G -->|Yes| H{F1/R1 Primers Valid?} + H -->|Yes| I[Full Credit Path] + H -->|No| F + C --> J[Final Score] + F --> J + I --> J ``` ## Component Relationships +The landing page and runtime page are defined in [index.html](../../index.html) and [core/systemrun.html](../../core/systemrun.html), with scripts in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) and [core/scripts/login.js](../../core/scripts/login.js). + ```mermaid graph LR - A["index.html
(Entry Point)"] - B["crispr_scripts.js
(Validation & UI)"] - C["login.js
(Auth & Account)"] - D["style.css
(Styling)"] - E["Benchling
gRNA Outputs"] - F["Gene Background
Info"] - - A -->|loads| B - A -->|loads| C - A -->|includes| D - B -->|fetches| E - B -->|fetches| F - C -->|depends on| B + A["Landing Page"] + B["Runtime Page"] + C["Client Scripts"] + D["Styling"] + E["gRNA Data"] + F["Gene Background Data"] + + A -->|navigates| B + B -->|loads| C + B -->|includes| D + C -->|fetches| E + C -->|fetches| F ``` ## Offline Support -Service worker configuration in [workbox-config.js](../../workbox-config.js) enables: - -- Offline browsing of cached pages -- Cached static assets (CSS, JS, images) -- Note: Dynamic gene data requires internet connection on first load +Service workers are registered in [index.html](../../index.html) and [core/systemrun.html](../../core/systemrun.html). The generated worker [core/scripts/serviceWorker/sw.js](../../core/scripts/serviceWorker/sw.js) precaches the core assets listed in [workbox-config.js](../../workbox-config.js) and applies runtime caching for HTML, CSS, JavaScript, and image requests. ## Dependencies ### Frontend Libraries -Located in [core/scripts/APIandLibraries/](../../core/scripts/APIandLibraries/): +Loaded by the runtime page [core/systemrun.html](../../core/systemrun.html): -- **jQuery** - DOM manipulation and AJAX -- **Bootstrap** - CSS grid and utilities -- **tabletoCSV** - Export functionality (optional) -- **Material Icons** - Icon fonts +- **jQuery** - Local script from [core/scripts/APIandLibraries/jQuery/](../../core/scripts/APIandLibraries/jQuery/) +- **Bootstrap** - Local script and styles from [core/scripts/APIandLibraries/Bootstrap/](../../core/scripts/APIandLibraries/Bootstrap/) +- **tabletoCSV** - Local script from [core/scripts/APIandLibraries/tabletoCSV/](../../core/scripts/APIandLibraries/tabletoCSV/) +- **Material Icons** - Google Fonts stylesheet in [core/systemrun.html](../../core/systemrun.html) ### Development Tools @@ -220,13 +225,13 @@ From [package.json](../../package.json): ## Security Considerations -1. **Content Security Policy** - Defined in [index.html](../../index.html) meta tags -2. **HTTPS Recommended** - Production should use HTTPS (Strict-Transport-Security header included) -3. **Input Validation** - Form inputs validated client-side and by marking algorithm +1. **Content Security Policy** - Defined in meta tags in [index.html](../../index.html) and [core/systemrun.html](../../core/systemrun.html) +2. **Strict-Transport-Security** - Defined in meta tags in [index.html](../../index.html) and [core/systemrun.html](../../core/systemrun.html) +3. **Input Validation** - Form inputs are checked by the client-side marking functions in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) ## Performance Optimizations -1. **Lazy Loading** - Gene data loaded on demand -2. **Minified Assets** - Pre-built minified versions available -3. **Service Worker Caching** - Static assets cached for offline access -4. **Client-side Rendering** - No server-side page generation overhead +1. **Runtime Data Fetch** - Gene data is fetched when `redirectCRISPR()` runs in [core/scripts/login.js](../../core/scripts/login.js) +2. **Minified Assets** - Pre-built minified versions are available in [core/scripts/](../../core/scripts/) and [core/styling/](../../core/styling/) +3. **Service Worker Caching** - Runtime caching rules are defined in [workbox-config.js](../../workbox-config.js) +4. **Client-side Rendering** - UI is generated in the browser by [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) diff --git a/docs/guides/data-structures.md b/docs/guides/data-structures.md index 4b797b4..ae7b8a9 100644 --- a/docs/guides/data-structures.md +++ b/docs/guides/data-structures.md @@ -4,7 +4,7 @@ This document describes the JSON data formats and data structures used throughou ## Overview -SciGrade uses JSON as its primary data format for gene information and gRNA validation reference data. These files are loaded client-side at application startup. +SciGrade uses JSON as its primary data format for gene information and guide RNA (gRNA) validation reference data. These files are loaded client-side during the runtime UI flow in [core/scripts/login.js](../../core/scripts/login.js) and [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ## Gene Background Information @@ -16,12 +16,12 @@ SciGrade uses JSON as its primary data format for gene information and gRNA vali ```json { - "_id": "5a67577c01ac2022a0eb6f56", - "owner_id": "5a4cb9e58f25b9cd6d49e868", - "number": 42, - "version": "0.3", - "date": "2018-08-20:1925", - "gene_list": {} + "_id": "5a67577c01ac2022a0eb6f56", + "owner_id": "5a4cb9e58f25b9cd6d49e868", + "number": 42, + "version": "0.3", + "date": "2018-08-20:1925", + "gene_list": {} } ``` @@ -37,17 +37,17 @@ SciGrade uses JSON as its primary data format for gene information and gRNA vali ```json { - "gene_list": { - "GENENAME": { - "base_type": "practice", - "name": "Full Gene Name", - "Background": "Educational description...", - "Target site": "Nucleotide position X - description of target", - "Target position": "123", - "Sequence": "ACGTACGT...(full sequence)...ACGT", - "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/12345" - } - } + "gene_list": { + "GENENAME": { + "base_type": "practice", + "name": "Full Gene Name", + "Background": "Educational description...", + "Target site": "Nucleotide position X - description of target", + "Target position": "123", + "Sequence": "ACGTACGT...(full sequence)...ACGT", + "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/12345" + } + } } ``` @@ -69,15 +69,15 @@ From actual data (HBB gene): ```json { - "HBB": { - "base_type": "practice", - "name": "Sickle cell anemia", - "Background": "Sickle cell anaemia is caused by an SNP in the human haemoglobin beta-chain which results in a GAG codon being replaced with a GTG codon (A → T)...", - "Target site": "Nucleotide position 73 - You are trying to change a thymine back to an alanine (WILD-TYPE).", - "Target position": "73", - "Sequence": "ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC", - "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/3043" - } + "HBB": { + "base_type": "practice", + "name": "Sickle cell anemia", + "Background": "Sickle cell anaemia is caused by an SNP in the human haemoglobin beta-chain which results in a GAG codon being replaced with a GTG codon (A → T)...", + "Target site": "Nucleotide position 73 - You are trying to change a thymine back to an alanine (WILD-TYPE).", + "Target position": "73", + "Sequence": "ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC", + "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/3043" + } } ``` @@ -91,12 +91,12 @@ From actual data (HBB gene): ```json { - "_id": "5a8deb6a547dd8319415ac3d", - "owner_id": "5a4cb9e58f25b9cd6d49e868", - "number": 42, - "version": "0.2", - "date": "2018-02-21:1657", - "gene_list": {} + "_id": "5a8deb6a547dd8319415ac3d", + "owner_id": "5a4cb9e58f25b9cd6d49e868", + "number": 42, + "version": "0.2", + "date": "2018-02-21:1657", + "gene_list": {} } ``` @@ -106,18 +106,18 @@ From actual data (HBB gene): ```json { - "gene_list": { - "GENENAME": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] - } + "gene_list": { + "GENENAME": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] + } } ``` @@ -138,24 +138,24 @@ From actual data (HBB gene): ```json { - "HBB": [ - { - "Position": 14, - "Strand": -1, - "Sequence": "AGTGAACACAGTTGTGTCAG", - "PAM": "AAG", - "Specificity Score": 39.0941742, - "Efficiency Score": 10.10900644 - }, - { - "Position": 17, - "Strand": -1, - "Sequence": "GCTAGTGAACACAGTTGTGT", - "PAM": "CAG", - "Specificity Score": 40.4041049, - "Efficiency Score": 22.38758304 - } - ] + "HBB": [ + { + "Position": 14, + "Strand": -1, + "Sequence": "AGTGAACACAGTTGTGTCAG", + "PAM": "AAG", + "Specificity Score": 39.0941742, + "Efficiency Score": 10.10900644 + }, + { + "Position": 17, + "Strand": -1, + "Sequence": "GCTAGTGAACACAGTTGTGT", + "PAM": "CAG", + "Specificity Score": 40.4041049, + "Efficiency Score": 22.38758304 + } + ] } ``` @@ -163,17 +163,11 @@ From actual data (HBB gene): **Specificity Score (Off-target):** -- Range: 0-100 (or higher with some algorithms) -- Meaning: Probability of cutting only the intended target -- Higher score = more specific (fewer off-target sites) -- Used by marking algorithm to validate student choice +- Used by the marking logic in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) **Efficiency Score (On-target):** -- Range: 0-100 -- Meaning: Likelihood of successfully cutting the target -- Higher score = more efficient cleavage -- Informational only (not used in current marking) +- Stored in the data file and not referenced by the marking logic in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) ## Additional Data Files @@ -183,8 +177,8 @@ From actual data (HBB gene): **Files:** -- `ACTN3.fasta` - Raw sequence in FASTA format -- `HBB.fasta` - Raw sequence in FASTA format +- [core/data/ACTN3/ACTN3.fasta](../../core/data/ACTN3/ACTN3.fasta) - Raw sequence in FASTA format +- [core/data/HBB/HBB.fasta](../../core/data/HBB/HBB.fasta) - Raw sequence in FASTA format - Similar files for other genes **Purpose:** Backup reference sequences (not actively used in current application). @@ -196,41 +190,21 @@ From actual data (HBB gene): ACGTACGTACGTACGTACGTACGTACGTACGT ``` -## Data Validation - -### Consistency Checks - -When loading data, verify: - -1. **Target Position Exists** in `gene_background_info.json` - - Must be a valid integer - - Must be within sequence length - -2. **gRNA Sequences Match Expected Length** - - Sequences should be 20bp (stored in Benchling outputs) - - PAM should be 3bp - -3. **Strand Values are Valid** - - Must be `1` (sense) or `-1` (antisense) - -4. **Scores are Numeric** - - Specificity and Efficiency scores should be floats - ### Loading Implementation In [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js): ```javascript async function loadCRISPRJSON_Files() { - try { - const responseBenchling = await fetch("./data/Benchling_gRNA_Outputs.json"); - benchling_gRNA_outputs = await responseBenchling.json(); - - const responseGeneBackground = await fetch("data/Background_info/gene_background_info.json"); - gene_backgroundInfo = await responseGeneBackground.json(); - } catch (err) { - console.error("Error fetching file:", err); - } + try { + const responseBenchling = await fetch("./data/Benchling_gRNA_Outputs.json"); + benchling_gRNA_outputs = await responseBenchling.json(); + + const responseGeneBackground = await fetch("data/Background_info/gene_background_info.json"); + gene_backgroundInfo = await responseGeneBackground.json(); + } catch (err) { + console.error("Error fetching file:", err); + } } ``` @@ -252,45 +226,17 @@ From [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) `loa ### Submission Processing +Submission processing is implemented in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). + ```mermaid graph TD A[Form Submission] --> B["Retrieve Input Values
from HTML Form"] B --> C["checkAnswers()"] - C --> D["Global Variables Set
MARgRNAseq, MARstrand, etc."] - D --> E["markAnswers()"] - E --> F["Calculate Final Score"] - F --> G["showFeedback()"] - G --> H["Display Results to Student"] - H --> I["Optional: Save to LocalStorage"] -``` - -## Browser Storage - -### LocalStorage Usage - -Application may store in browser `localStorage`: - -- Session state -- Recent submissions -- User preferences - -**Access in JavaScript:** - -```javascript -localStorage.setItem("key", value); -const retrieved = localStorage.getItem("key"); -localStorage.removeItem("key"); -``` - -### Session Variables - -Global variables in [crispr_scripts.js](../../core/scripts/crispr_scripts.js): - -```javascript -let selection_inMode = "practice"; // Current mode -let current_gene = "empty"; // Selected gene -let loadedMode = "practice"; // Last loaded mode -let checkAnswers_executed = false; // Submission state + C --> D["Global Variables Set"] + D --> E["markAnswers()"] + E --> F["Calculate Final Score"] + F --> G["showFeedback()"] + G --> H["Display Results to Student"] ``` ## Adding New Genes @@ -301,15 +247,15 @@ To add a new gene to SciGrade: ```json { - "NEWGENE": { - "base_type": "practice", - "name": "Gene Full Name", - "Background": "Educational description...", - "Target site": "Nucleotide position X - description", - "Target position": "123", - "Sequence": "ACGT... full sequence ...", - "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/..." - } + "NEWGENE": { + "base_type": "practice", + "name": "Gene Full Name", + "Background": "Educational description...", + "Target site": "Nucleotide position X - description", + "Target position": "123", + "Sequence": "ACGT... full sequence ...", + "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/..." + } } ``` @@ -317,21 +263,26 @@ To add a new gene to SciGrade: ```json { - "NEWGENE": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] + "NEWGENE": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] } ``` **To Verify:** - Gene appears in dropdown: [fillGeneList()](../../core/scripts/crispr_scripts.js#L60) -- Assignment loads correctly: [loadWork()](../../core/scripts/crispr_scripts.js#L82) +- Form loads correctly: [loadWork()](../../core/scripts/crispr_scripts.js#L82) - Tests pass: `npm run test` + +## Related Documentation + +- [Marking Algorithm](marking-algorithm.md) - Validation flow and scoring +- [API Reference](../api/index.md) - Function reference for data loading diff --git a/docs/guides/marking-algorithm.md b/docs/guides/marking-algorithm.md index 05c7ad4..d2842ce 100644 --- a/docs/guides/marking-algorithm.md +++ b/docs/guides/marking-algorithm.md @@ -1,27 +1,20 @@ # Marking Algorithm -This document explains how gRNA sequences and primers are validated and scored in SciGrade. +This document explains how guide RNA (gRNA) sequences and primers are validated and scored in SciGrade. ## Overview The marking system validates student submissions across five key components: -1. **gRNA Sequence** - Must match a reference sequence -2. **PAM Sequence** - Must match the PAM of the validated gRNA +1. **guide RNA (gRNA) Sequence** - Must match a reference sequence +2. **Protospacer Adjacent Motif (PAM) Sequence** - Must match the PAM of the validated gRNA 3. **Strand** - Must indicate correct strand (sense/antisense) 4. **Off-target Score** - Must meet an "optimal" threshold 5. **F1 & R1 Primers** - Must be correctly designed with proper complementarity ## Core Marking Function -The main marking logic is in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js): - -```javascript -function markAnswers() { - // Marking is based on checkAnswers() results - // Returns a combined score from individual component checks -} -``` +The main marking logic is implemented in `markAnswers()` in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ## Step-by-Step Validation @@ -29,13 +22,13 @@ function markAnswers() { ```mermaid sequenceDiagram - crispr_scripts.js->>Benchling_gRNA_Outputs.json: loadCRISPRJSON_Files() - Benchling_gRNA_Outputs.json-->>crispr_scripts.js: benchling_gRNA_outputs - crispr_scripts.js->>gene_background_info.json: loadCRISPRJSON_Files() - gene_background_info.json-->>crispr_scripts.js: gene_backgroundInfo + UI->>gRNAData: loadCRISPRJSON_Files() + gRNAData-->>UI: benchling_gRNA_outputs + UI->>GeneInfo: loadCRISPRJSON_Files() + GeneInfo-->>UI: gene_backgroundInfo ``` -Both reference files are fetched asynchronously during initialization. +Both reference files are fetched asynchronously during initialization from [core/data/Benchling_gRNA_Outputs.json](../../core/data/Benchling_gRNA_Outputs.json) and [core/data/Background_info/gene_background_info.json](../../core/data/Background_info/gene_background_info.json) by [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ### Step 2: gRNA Sequence Validation @@ -44,16 +37,16 @@ When a student submits their answer, [checkAnswers()](../../core/scripts/crispr_ ```javascript const inputtedSeq = document.getElementById("sequence_input").value.trim(); for (const answer of benchling_gRNA_outputs.gene_list[current_gene]) { - if (answer.Sequence === inputtedSeq) { - possible_comparable_answers.push(answer); - } + if (answer.Sequence === inputtedSeq) { + possible_comparable_answers.push(answer); + } } ``` **Matching Criteria:** -- Input sequence must **exactly match** one or more reference sequences (case-insensitive after trim) -- If no match found, all components are marked incorrect +- Input sequence must **exactly match** one or more reference sequences (case-sensitive after trim) +- If no match found, the downstream validation steps are skipped - If matches found, continue to step 3 ### Step 3: Nucleotide Target Validation @@ -64,35 +57,33 @@ For each possible matching sequence, verify the target nucleotide is within the const correctNucleotidePosition = gene_backgroundInfo.gene_list[current_gene]["Target position"] - 1; if (possibleAnswer.Strand === 1) { - // Sense strand: check if target is within gRNA range - const nucleotideIncludedRange_top = possibleAnswer.Position - 1 - 1 + 3; - const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 17; - - if ( - correctNucleotidePosition >= nucleotideIncludedRange_bot && - correctNucleotidePosition <= nucleotideIncludedRange_top - ) { - correctNucleotideIncluded = true; - } + // Sense strand: check if target is within gRNA range + const nucleotideIncludedRange_top = possibleAnswer.Position - 1 - 1 + 3; + const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 17; + + if ( + correctNucleotidePosition >= nucleotideIncludedRange_bot && + correctNucleotidePosition <= nucleotideIncludedRange_top + ) { + correctNucleotideIncluded = true; + } } else if (possibleAnswer.Strand === -1) { - // Antisense strand: check if target is within gRNA range - const nucleotideIncludedRange_top = possibleAnswer.Position - 1 + 17; - const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 3; - - if ( - correctNucleotidePosition >= nucleotideIncludedRange_bot && - correctNucleotidePosition <= nucleotideIncludedRange_top - ) { - correctNucleotideIncluded = true; - } + // Antisense strand: check if target is within gRNA range + const nucleotideIncludedRange_top = possibleAnswer.Position - 1 + 17; + const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 3; + + if ( + correctNucleotidePosition >= nucleotideIncludedRange_bot && + correctNucleotidePosition <= nucleotideIncludedRange_top + ) { + correctNucleotideIncluded = true; + } } ``` **Why This Matters:** -- The gRNA must include the target mutation -- 20bp gRNA covers ~17-20 nucleotides depending on strand -- If target is outside this range, the gRNA cannot affect the mutation +- The target position must fall within the strand-specific range calculated in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) ### Step 4: Strand Validation @@ -100,13 +91,13 @@ Check if the student selected the correct strand: ```javascript if (possibleAnswer.Strand === 1) { - if (document.getElementById("strand_input").value === "Sense (+)") { - MARstrand = true; - } + if (document.getElementById("strand_input").value === "Sense (+)") { + MARstrand = true; + } } else if (possibleAnswer.Strand === -1) { - if (document.getElementById("strand_input").value === "Antisense (-)") { - MARstrand = true; - } + if (document.getElementById("strand_input").value === "Antisense (-)") { + MARstrand = true; + } } ``` @@ -116,121 +107,58 @@ if (possibleAnswer.Strand === 1) { - Strand `-1` = Antisense (-) strand ### Step 5: PAM Sequence Validation - -PAM location depends on strand orientation: - -```javascript -if (possibleAnswer.Strand === 1) { - pamFirst = possibleAnswer.Position - 1 + 2; - pamSecond = possibleAnswer.Position - 1 + 4; -} else if (possibleAnswer.Strand === -1) { - pamFirst = possibleAnswer.Position - 1 - 2; - pamSecond = possibleAnswer.Position - 1 - 4; -} - -// Extract PAM from sequence -const pamExtracted = gene_backgroundInfo.gene_list[current_gene].Sequence.slice(pamFirst, pamSecond + 1); - -// Check if student input matches -if (document.getElementById("pam_input").value === possibleAnswer.PAM) { - MARPAMseq = true; -} -``` +PAM validation compares the student's input to the `PAM` value on the matched reference entry in [core/data/Benchling_gRNA_Outputs.json](../../core/data/Benchling_gRNA_Outputs.json) as implemented in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ### Step 6: Off-Target Score Validation ```javascript function checkOffTarget(score) { - // Check if off-target score meets minimum threshold - // Threshold depends on marking mode settings + // Check if off-target score meets minimum threshold + // Threshold depends on marking mode settings } ``` **Scoring Modes:** -The off-target score is validated against an "optimal" value: - -1. **Optimal Mode** (default): - - ``` - Min_optimal = Max_range - (Max_range * 0.2) - ``` +The off-target score uses the following steps in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js): - Where `Max_range` is the highest feasible off-target score for the gene. - -2. **Custom Mode**: - - TA/Admin sets a custom optimal value between 0.01 and 100 - - Student score must exceed this custom value +1. Build a list of reference scores within +/- 35 positions of the submitted cut position. +2. Compute `Max_range` from that list and `Min_optimal = Max_range - (Max_range * 0.2)`. +3. When the class marking mode is `Optimal`, use 80 as the threshold if `Min_optimal` is greater than 80 or less than 35. +4. When the class marking mode is `Custom`, use the class-specific value stored in `student_reg_information`. **Pass Criteria:** -- Score > optimal value = Full credit (mark as above optimal) -- Score > 35 but ≤ optimal = Partial credit (above minimum) -- Score > 0 but ≤ 35 = Minimal credit (technically feasible) +- Input at or above the optimal threshold sets `MAROffTarget_degree` to `1`. +- Input at or above 35 sets `MAROffTarget_degree` to `2` when `Max_range` is at least 80. +- If the local max score is below 35, the input is treated as the only option and sets `MAROffTarget_degree` to `3`. ### Step 7: Primer Validation #### F1 Primer Check - -```javascript -function checkF1Primers(seq) { - // F1 (forward) primer structure - // Typically includes promoter sequence + T7 binding + gRNA start - // Student input should contain required segments -} -``` +The F1 primer is validated by building candidate primers with the `TAATACGACTCACTATAG` prefix and the first 16-20 bases of the submitted gRNA sequence in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). #### R1 Primer Check - -```javascript -function checkR1Primers(seq) { - // R1 (reverse) primer must be reverse complement of gRNA - const complement = createComplementarySeq(seq); - // Check if sequence contains complement within correct region -} -``` - -**Complementarity Function:** - -```javascript -function createComplementarySeq(seq) { - // A ↔ T, G ↔ C, then reverse the string - let complement = ""; - for (const base of seq) { - if (base === "A") complement += "T"; - else if (base === "T") complement += "A"; - else if (base === "G") complement += "C"; - else if (base === "C") complement += "G"; - } - return complement.split("").reverse().join(""); -} -``` +The R1 primer is validated by building a reverse-complement string and then constructing candidate primers with the `TTCTAGCTCTAAAAC` prefix and the first 19-20 bases of the reverse complement in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ## Scoring Logic ```mermaid flowchart TD - A[Student Submission] --> B["Check gRNA Sequence
MARgRNAseq"] - B -->|Match Found| C["Validate Strand
MARstrand"] - B -->|No Match| D["All Components WRONG"] - C -->|Correct| E["Validate Target Position
correctNucleotideIncluded"] - C -->|Incorrect| D - E -->|In Range| F["Validate PAM
MARPAMseq"] - E -->|Out of Range| D - F -->|Correct| G["Validate Off-target
MAROffTarget"] - F -->|Incorrect| D - G -->|Valid| H["Validate Primers
MARF1primers, MARR1primers"] - G -->|Invalid| I["Off-target WRONG
Primers Check Anyway"] - H -->|All Correct| J[Full Mark] - H -->|Some Correct| K[Partial Mark] - H -->|None Correct| L[No Mark on Primers] - I --> K - I --> L - D --> M[Score = 0] - J --> N[Final Score Calculated] - K --> N - L --> N - M --> N + A[Student Submission] --> B["Match gRNA Sequence"] + B -->|Match Found| C["Validate Strand and Target Range"] + B -->|No Match| D["No gRNA Credit"] + C -->|Valid| E["Validate PAM"] + C -->|Invalid| D + E -->|Valid| F["Validate Off-target"] + E -->|Invalid| G["Partial Credit Path"] + F -->|Valid| H["Validate Primers"] + F -->|Invalid| G + H -->|All Correct| I["Full Credit Path"] + H -->|Some Wrong| G + D --> J["Final Score"] + G --> J + I --> J ``` ## Global State Variables @@ -244,31 +172,28 @@ let MARPAMseq = false; // PAM sequence match let MARCutPos = false; // Cut position correctness let MARstrand = false; // Strand selection correctness let MAROffTarget = false; // Off-target score validity -let MAROffTarget_degree = 0; // 0: wrong, 1: >75, 2: >35, 3: only option +let MAROffTarget_degree = 0; // 0: wrong, 1: optimal/above, 2: >=35 below optimal, 3: only option let MARF1primers = false; // F1 primer correctness let MARR1primers = false; // R1 primer correctness ``` ## Feedback System -After marking, student feedback is displayed via [showFeedback()](../../core/scripts/crispr_scripts.js#L602): +After marking, student feedback is displayed via [showFeedback()](../../core/scripts/crispr_scripts.js): ```mermaid sequenceDiagram markAnswers->>showFeedback: Pass marking results showFeedback->>Student: Display component scores - showFeedback->>Student: Show correct answers - showFeedback->>Student: Explain errors - showFeedback->>LocalStorage: Cache results + showFeedback->>Student: Show feedback details + showFeedback->>Student: Explain scoring ``` **Feedback Includes:** - Component-by-component results (✓ or ✗) -- Correct gRNA sequence if wrong -- Correct PAM if wrong -- Optimal off-target threshold -- Primer design suggestions +- Explanatory text generated from the current marking state +- Candidate primer lists derived from the submitted gRNA sequence ## Customization @@ -277,12 +202,12 @@ sequenceDiagram In account management modal (opened via [openAccountManagement()](../../core/scripts/crispr_scripts.js#L853)): 1. Select "Optimal" mode: - - Automatically calculates: `Max - (Max * 0.2)` - - Applies to all students in class + - Calculates `Min_optimal = Max_range - (Max_range * 0.2)` from nearby scores + - Uses 80 as the threshold when `Min_optimal` is greater than 80 or less than 35 2. Select "Custom" mode: - Enter specific value (0.01 - 100) - - Allows flexible grading standards + - Stored in `student_reg_information[0].classMarkingMod` for the selected class ### Adding Custom Marking Rules @@ -299,18 +224,18 @@ Ensure reference data in [Benchling_gRNA_Outputs.json](../../core/data/Benchling ```json { - "gene_list": { - "GENENAME": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] - } + "gene_list": { + "GENENAME": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] + } } ``` @@ -332,3 +257,8 @@ Run tests: ```bash npm run test:jest ``` + +## Related Documentation + +- [Data Structures](data-structures.md) - JSON reference inputs +- [API Reference](../api/index.md) - Function reference for marking diff --git a/docs/guides/setup.md b/docs/guides/setup.md index fa2f969..2147280 100644 --- a/docs/guides/setup.md +++ b/docs/guides/setup.md @@ -2,7 +2,7 @@ ## System Requirements -- **Node.js**: 14+ (includes npm) +- **Node.js**: 20+ - **Browser**: Chrome, Firefox, Edge, or Safari with ES6+ support ## Installation @@ -20,7 +20,7 @@ cd SciGrade npm ci ``` -This installs exact dependency versions from `package-lock.json` (generated from [package.json](../../package.json)). +This installs exact dependency versions from [package-lock.json](../../package-lock.json) (generated from [package.json](../../package.json)). ### 3. Start Local Server @@ -44,7 +44,7 @@ npm run prettier:check # Check code formatting npm run prettier # Format code automatically # Testing -npm run test # Run all tests (jest + playwright) +npm run test # Run jest unit tests npm run test:jest # Run jest unit tests only npm run test:playwright:headless # Run playwright tests headless npm run test:playwright:ui # Run playwright tests in UI mode @@ -58,34 +58,28 @@ npm run workbox # Generate service worker with workbox ## Project Structure -```text -/core - /data # JSON data files - /Background_info # Gene background information - Benchling_gRNA_Outputs.json # gRNA validation reference data - /scripts - /APIandLibraries # Third-party libraries (jQuery, Bootstrap) - /serviceWorker # Service worker for offline support - crispr_scripts.js # Main gRNA/primer validation logic - login.js # Authentication and user management - /styling - style.css # Application styles - /images # SVG and PNG assets - /icon # PWA icons and manifest - index.html # Main entry point - -/docs # Documentation (this directory) -/tests - /jest # Jest unit test configuration - /playwright # Playwright E2E test configuration -/test-results # Test output directory - -package.json # Dependencies and scripts -jest.config.mjs # Jest configuration -playwright.config.js # Playwright configuration -eslint.config.js # ESLint configuration -.prettierrc # Prettier configuration -``` +- [core/](../../core/) - Application assets and scripts +- [core/data/](../../core/data/) - JSON data files +- [core/data/Background_info/](../../core/data/Background_info/) - Gene background information +- [core/data/Benchling_gRNA_Outputs.json](../../core/data/Benchling_gRNA_Outputs.json) - guide RNA (gRNA) validation reference data +- [core/scripts/](../../core/scripts/) - Client-side scripts +- [core/scripts/APIandLibraries/](../../core/scripts/APIandLibraries/) - Third-party libraries (jQuery, Bootstrap) +- [core/scripts/serviceWorker/](../../core/scripts/serviceWorker/) - Service worker runtime +- [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js) - Main gRNA/primer validation logic +- [core/scripts/login.js](../../core/scripts/login.js) - Login and account helpers +- [core/styling/style.css](../../core/styling/style.css) - Application styles +- [core/images/](../../core/images/) - SVG and PNG assets +- [core/icon/](../../core/icon/) - PWA icons and manifest +- [index.html](../../index.html) - Landing page with Start link +- [core/systemrun.html](../../core/systemrun.html) - Application runtime entry +- [docs/](../) - Documentation directory +- [tests/](../../tests/) - Test suites +- [test-results/](../../test-results/) - Test output directory +- [package.json](../../package.json) - Dependencies and scripts +- [jest.config.mjs](../../jest.config.mjs) - Jest configuration +- [playwright.config.js](../../playwright.config.js) - Playwright configuration +- [eslint.config.js](../../eslint.config.js) - ESLint configuration +- [.prettierrc](../../.prettierrc) - Prettier configuration ## Configuration Files @@ -101,17 +95,17 @@ Structure: ```json { - "gene_list": { - "GENENAME": { - "base_type": "practice|assignment", - "name": "Full Gene Name", - "Background": "Description of gene and mutation", - "Target site": "Location and nature of target", - "Target position": "Numeric position", - "Sequence": "ACGT... full DNA sequence", - "NCBI gene link": "https://..." - } - } + "gene_list": { + "GENENAME": { + "base_type": "practice|assignment", + "name": "Full Gene Name", + "Background": "Description of gene and mutation", + "Target site": "Location and nature of target", + "Target position": "Numeric position", + "Sequence": "ACGT... full DNA sequence", + "NCBI gene link": "https://..." + } + } } ``` @@ -138,20 +132,6 @@ Structure: } ``` -### Environment Configuration - -#### Practice Mode by Default - -The application is configured for practice mode where students can use SciGrade without any authentication system. - -To enable authentication (for local deployment only), edit [core/scripts/login.js](../../core/scripts/login.js) line ~10: - -```javascript -let continueWithoutLogin = false; -``` - -**Note:** The online authentication features were deprecated in v1.2.0. See [CHANGELOG.md](../../CHANGELOG.md) for details. - ## Testing ### Jest Unit Tests @@ -201,8 +181,6 @@ Minified versions are pre-built: - [core/scripts/login.min.js](../../core/scripts/login.min.js) - [core/styling/style.min.css](../../core/styling/style.min.css) -These are generated through your build pipeline (outside the npm scripts). - ## Troubleshooting ### Port 3000 Already in Use @@ -224,7 +202,7 @@ npm run regen-package-lock - Clear browser cache and service worker registration - In DevTools: Application > Service Workers > Unregister -## Next Steps +## Related Documentation - Read [../architecture/index.md](../architecture/index.md) for system design - Review [../guides/marking-algorithm.md](../guides/marking-algorithm.md) for validation logic diff --git a/docs/index.md b/docs/index.md index b6f83b5..b659bbb 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,7 +4,9 @@ Welcome to the SciGrade documentation. This directory contains comprehensive gui ## Overview -[SciGrade](https://scigrade.com/) is an online web-tool that allows students and educators to practice and receive feedback on gRNA (guide RNA) design and F1/R1 primer generation for CRISPR-based genetic modifications. +[SciGrade](https://scigrade.com/) is a client-side web application that allows students and educators to practice and receive feedback on guide RNA (gRNA) design and F1/R1 primer entry for Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based workflows. + +The landing page is [index.html](../index.html), which links to the application runtime page [core/systemrun.html](../core/systemrun.html). The runtime page loads the app scripts [core/scripts/login.min.js](../core/scripts/login.min.js) and [core/scripts/crispr_scripts.min.js](../core/scripts/crispr_scripts.min.js) and starts the UI flow on page load. ## Documentation Structure @@ -16,80 +18,79 @@ Welcome to the SciGrade documentation. This directory contains comprehensive gui ## Application Flow +The flow below reflects the landing page in [index.html](../index.html) and the runtime UI/data flow in [core/scripts/login.js](../core/scripts/login.js) and [core/scripts/crispr_scripts.js](../core/scripts/crispr_scripts.js). + ```mermaid flowchart TD - A["User Loads Page
(index.html or systemrun.html)"] --> B["Load Scripts
(crispr_scripts.js
login.js)"] - B --> C["Load JSON Data
(gene_background_info.json
Benchling_gRNA_Outputs.json)"] - C --> D["Populate Gene
Dropdown"] - D --> E["User Selects Gene"] - E --> F["Render Assignment
Form"] - F --> G{"User Submits
Answer?"} - G -->|Yes| H["Validate Answers
(checkAnswers)"] - H --> I["Calculate Score
(markAnswers)"] - I --> J["Display Feedback"] - J --> K["Show Results"] - G -->|No| E - K --> L["End Session"] + A["User Loads Landing Page"] --> B["Start Button Navigates to App Page"] + B --> C["App Page Loads Scripts"] + C --> D["Fetch JSON Data"] + D --> E["Populate Gene Dropdown"] + E --> F["User Selects Gene"] + F --> G["Render Input Form"] + G --> H{"User Submits Answers?"} + H -->|Yes| I["Validate Answers"] + I --> J["Calculate Score"] + J --> K["Show Feedback"] + H -->|No| F ``` ## User Interaction Sequence +This sequence follows the runtime flow implemented in [core/scripts/login.js](../core/scripts/login.js) and [core/scripts/crispr_scripts.js](../core/scripts/crispr_scripts.js). + ```mermaid sequenceDiagram participant User participant Browser - participant crispr_scripts.js - participant JSON Data - - User->>Browser: Load SciGrade - Browser->>crispr_scripts.js: Execute scripts - crispr_scripts.js->>JSON Data: Fetch gene data - JSON Data-->>crispr_scripts.js: Return data - crispr_scripts.js->>Browser: Populate gene list - User->>Browser: Select gene & click Load - Browser->>crispr_scripts.js: loadGeneContent() - crispr_scripts.js->>Browser: Render form + participant UI + participant Data + + User->>Browser: Load landing page + User->>Browser: Click Start + Browser->>UI: Build selection UI + UI->>Data: Fetch gene data + Data-->>UI: Return data + UI->>Browser: Populate gene list + User->>Browser: Select gene & click Load Gene + Browser->>UI: Render input form User->>Browser: Enter gRNA + primers User->>Browser: Click Submit - Browser->>crispr_scripts.js: submitAnswers() - crispr_scripts.js->>crispr_scripts.js: checkAnswers() - crispr_scripts.js->>crispr_scripts.js: markAnswers() - crispr_scripts.js->>Browser: Display feedback + Browser->>UI: Validate answers + UI->>Browser: Display feedback ``` ## Key Concepts ### Genes -SciGrade supports multiple target genes for practice and assignment work: +SciGrade uses the gene list defined in [core/data/Background_info/gene_background_info.json](../core/data/Background_info/gene_background_info.json): -- **eBFP** - Enhanced blue fluorescence protein (HEK293FT cells) -- **ACTN3** - Actinin alpha 3 (elite athletic performance mutation) +- **eBFP** - Enhanced blue fluorescence protein +- **ACTN3** - Actinin alpha 3 - **HBB** - Hemoglobin beta (sickle cell anemia) - **CCR5** - C-C motif chemokine receptor 5 (HIV resistance) -- **ANKK1** - Ankyrin repeat and kinase domain-containing protein 1 - **APOE** - Apolipoprotein E (Alzheimer's risk) ### Core Features -#### Practice Mode +#### Practice Flow -- Students can freely experiment with gRNA and primer design -- Immediate feedback on submission -- No login required (by default) +- The runtime page initializes the UI without requiring authentication +- The runtime page initializes the UI without requiring authentication in [core/systemrun.html](../core/systemrun.html) +- Feedback is generated after submission by [core/scripts/crispr_scripts.js](../core/scripts/crispr_scripts.js) -#### Assignment Mode +#### Account Management UI -- Locally deployed version allows instructor use for grading -- Submission and result tracking -- No online account system required +- Account management and class tooling are present in the client-side scripts and hidden by default in [core/systemrun.html](../core/systemrun.html) +- The [CHANGELOG.md](../CHANGELOG.md) records the deprecation of online account features ## Technology Stack -- **Frontend**: Vanilla JavaScript, jQuery, Bootstrap -- **Data**: Client-side JSON data files -- **Build Tools**: Jest, Playwright, ESLint, Prettier -- **Service Worker**: Workbox for offline caching +- **Frontend**: Vanilla JavaScript with jQuery and Bootstrap loaded from [core/scripts/APIandLibraries/](../core/scripts/APIandLibraries/) +- **Data**: Client-side JSON data files loaded by [core/scripts/crispr_scripts.js](../core/scripts/crispr_scripts.js) +- **Build Tools**: Jest, Playwright, ESLint, and Prettier defined in [package.json](../package.json) +- **Service Worker**: Workbox configuration in [workbox-config.js](../workbox-config.js) and generated runtime in [core/scripts/serviceWorker/sw.js](../core/scripts/serviceWorker/sw.js) ## Development @@ -97,13 +98,9 @@ For contributions and modifications: 1. Review [CONTRIBUTING.md](../CONTRIBUTING.md) 2. Read [EDIT.MD](../EDIT.MD) for modification guidance -3. Follow [setup.md](guides/setup.md) for local development -4. Ensure all tests pass with `npm run validate` +3. Follow [guides/setup.md](guides/setup.md) for local development +4. Run `npm run validate` from [package.json](../package.json) ## License SciGrade is licensed under [GPL-3.0](../LICENSE.md) - -## Project Status - -This project is in **maintenance mode**. Only critical bug fixes and security updates will be addressed. diff --git a/package-lock.json b/package-lock.json index b766ff1..ac8397c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,18 +9,18 @@ "version": "1.2.0", "license": "GPL-3.0", "devDependencies": { - "@playwright/test": "^1.57.0", + "@playwright/test": "^1.58.2", "@types/jest": "^30.0.0", - "@types/node": "^25.0.3", + "@types/node": "^25.2.3", "axe-playwright": "^2.2.2", - "eslint": "^9.39.2", + "eslint": "^10.0.0", "eslint-config-prettier": "^10.1.8", - "eslint-plugin-prettier": "^5.5.4", - "globals": "^17.0.0", + "eslint-plugin-prettier": "^5.5.5", + "globals": "^17.3.0", "http-server": "^14.1.1", "jest": "^30.2.0", "jest-environment-jsdom": "^30.2.0", - "prettier": "^3.7.4", + "prettier": "^3.8.1", "workbox-cli": "^7.4.0" } }, @@ -46,13 +46,13 @@ "license": "ISC" }, "node_modules/@babel/code-frame": { - "version": "7.27.1", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.27.1.tgz", - "integrity": "sha512-cjQ7ZlQ0Mv3b47hABuTevyTuYN4i+loJKGeV9flcCgIK37cCXRh+L1bd3iBHlynerhQ7BhCkn2BPbQUL+rGqFg==", + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.0.tgz", + "integrity": "sha512-9NhCeYjq9+3uxgdtp20LSiJXJvN0FeCtNGpJxuMFZ1Kv3cWUNb6DOhJwUvcVCzKGR66cw4njwM6hrJLqgOwbcw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-validator-identifier": "^7.27.1", + "@babel/helper-validator-identifier": "^7.28.5", "js-tokens": "^4.0.0", "picocolors": "^1.1.1" }, @@ -61,9 +61,9 @@ } }, "node_modules/@babel/compat-data": { - "version": "7.28.5", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.5.tgz", - "integrity": "sha512-6uFXyCayocRbqhZOB+6XcuZbkMNimwfVGFji8CTZnCzOHVGvDqzvitu1re2AU5LROliz7eQPhB8CpAMvnx9EjA==", + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.29.0.tgz", + "integrity": "sha512-T1NCJqT/j9+cn8fvkt7jtwbLBfLC/1y1c7NtCeXFRgzGTsafi68MRv8yzkYSapBnFA6L3U2VSc02ciDzoAJhJg==", "dev": true, "license": "MIT", "engines": { @@ -71,22 +71,21 @@ } }, "node_modules/@babel/core": { - 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"peer": true, "bin": { "rollup": "dist/bin/rollup" }, @@ -10099,11 +9966,14 @@ } }, "node_modules/smob": { - "version": "1.5.0", - "resolved": "https://registry.npmjs.org/smob/-/smob-1.5.0.tgz", - "integrity": "sha512-g6T+p7QO8npa+/hNx9ohv1E5pVCmWrVCUzUXJyLdMmftX6ER0oiWY/w9knEonLpnOp6b6FenKnMfR8gqwWdwig==", + "version": "1.6.1", + "resolved": "https://registry.npmjs.org/smob/-/smob-1.6.1.tgz", + "integrity": "sha512-KAkBqZl3c2GvNgNhcoyJae1aKldDW0LO279wF9bk1PnluRTETKBq0WyzRXxEhoQLk56yHaOY4JCBEKDuJIET5g==", "dev": true, - "license": "MIT" + "license": "MIT", + "engines": { + "node": ">=20.0.0" + } }, "node_modules/source-map": { "version": "0.6.1", @@ -10595,9 +10465,9 @@ "license": "MIT" }, "node_modules/synckit": { - "version": "0.11.11", - "resolved": "https://registry.npmjs.org/synckit/-/synckit-0.11.11.tgz", - "integrity": "sha512-MeQTA1r0litLUf0Rp/iisCaL8761lKAZHaimlbGK4j0HysC4PLfqygQj9srcs0m2RdtDYnF8UuYyKpbjHYp7Jw==", + "version": "0.11.12", + "resolved": "https://registry.npmjs.org/synckit/-/synckit-0.11.12.tgz", + "integrity": "sha512-Bh7QjT8/SuKUIfObSXNHNSK6WHo6J1tHCqJsuaFDP7gP0fkzSfTxI8y85JrppZ0h8l0maIgc2tfuZQ6/t3GtnQ==", "dev": true, "license": "MIT", "dependencies": { @@ -10653,9 +10523,9 @@ } }, "node_modules/terser": { - 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"deprecated": "Glob versions prior to v9 are no longer supported", + "deprecated": "Old versions of glob are not supported, and contain widely publicized security vulnerabilities, which have been fixed in the current version. Please update. Support for old versions may be purchased (at exorbitant rates) by contacting i@izs.me", "dev": true, "license": "ISC", "dependencies": { @@ -10719,6 +10607,19 @@ "url": "https://github.com/sponsors/isaacs" } }, + "node_modules/test-exclude/node_modules/minimatch": { + "version": "3.1.2", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz", + "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==", + "dev": true, + "license": "ISC", + "dependencies": { + "brace-expansion": "^1.1.7" + }, + "engines": { + "node": "*" + } + }, "node_modules/through": { "version": "2.3.8", "resolved": "https://registry.npmjs.org/through/-/through-2.3.8.tgz", @@ -11158,9 +11059,9 @@ } }, "node_modules/update-notifier/node_modules/semver": { - "version": "7.7.3", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.3.tgz", - "integrity": "sha512-SdsKMrI9TdgjdweUSR9MweHA4EJ8YxHn8DFaDisvhVlUOe4BF1tLD7GAj0lIqWVl+dPb/rExr0Btby5loQm20Q==", + "version": "7.7.4", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.4.tgz", + "integrity": "sha512-vFKC2IEtQnVhpT78h1Yp8wzwrf8CM+MzKMHGJZfBtzhZNycRFnXsHk6E5TxIkkMsgNS7mdX3AGB7x2QM2di4lA==", "dev": true, "license": "ISC", "bin": { @@ -11392,9 +11293,9 @@ } }, "node_modules/which-typed-array": { - "version": "1.1.19", - "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.19.tgz", - "integrity": "sha512-rEvr90Bck4WZt9HHFC4DJMsjvu7x+r6bImz0/BrbWb7A2djJ8hnZMrWnHo9F8ssv0OMErasDhftrfROTyqSDrw==", + "version": "1.1.20", + "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.20.tgz", + "integrity": "sha512-LYfpUkmqwl0h9A2HL09Mms427Q1RZWuOHsukfVcKRq9q95iQxdw0ix1JQrqbcDR9PH1QDwf5Qo8OZb5lksZ8Xg==", "dev": true, "license": "MIT", "dependencies": { @@ -11552,13 +11453,22 @@ "ajv": ">=8" } }, + "node_modules/workbox-build/node_modules/@isaacs/cliui": { + "version": "9.0.0", + "resolved": "https://registry.npmjs.org/@isaacs/cliui/-/cliui-9.0.0.tgz", + "integrity": "sha512-AokJm4tuBHillT+FpMtxQ60n8ObyXBatq7jD2/JA9dxbDDokKQm8KMht5ibGzLVU9IJDIKK4TPKgMHEYMn3lMg==", + "dev": true, + "license": "BlueOak-1.0.0", + "engines": { + "node": ">=18" + } + }, "node_modules/workbox-build/node_modules/ajv": { - "version": "8.17.1", - "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.17.1.tgz", - "integrity": "sha512-B/gBuNg5SiMTrPkC+A2+cW0RszwxYmn6VYxB/inlBStS5nx6xHIt/ehKRhIMhqusl7a8LjQoZnjCs5vhwxOQ1g==", + "version": "8.18.0", + "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.18.0.tgz", + "integrity": "sha512-PlXPeEWMXMZ7sPYOHqmDyCJzcfNrUr3fGNKtezX14ykXOEIvyK81d+qydx89KY5O71FKMPaQ2vBfBFI5NHR63A==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "fast-deep-equal": "^3.1.3", "fast-uri": "^3.0.1", @@ -11574,6 +11484,7 @@ "version": "11.1.0", "resolved": "https://registry.npmjs.org/glob/-/glob-11.1.0.tgz", "integrity": "sha512-vuNwKSaKiqm7g0THUBu2x7ckSs3XJLXE+2ssL7/MfTGPLLcrJQ/4Uq1CjPTtO5cCIiRxqvN6Twy1qOwhL0Xjcw==", + "deprecated": "Old versions of glob are not supported, and contain widely publicized security vulnerabilities, which have been fixed in the current version. Please update. Support for old versions may be purchased (at exorbitant rates) by contacting i@izs.me", "dev": true, "license": "BlueOak-1.0.0", "dependencies": { @@ -11595,13 +11506,13 @@ } }, "node_modules/workbox-build/node_modules/jackspeak": { - "version": "4.1.1", - "resolved": "https://registry.npmjs.org/jackspeak/-/jackspeak-4.1.1.tgz", - "integrity": "sha512-zptv57P3GpL+O0I7VdMJNBZCu+BPHVQUk55Ft8/QCJjTVxrnJHuVuX/0Bl2A6/+2oyR/ZMEuFKwmzqqZ/U5nPQ==", + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/jackspeak/-/jackspeak-4.2.3.tgz", + "integrity": "sha512-ykkVRwrYvFm1nb2AJfKKYPr0emF6IiXDYUaFx4Zn9ZuIH7MrzEZ3sD5RlqGXNRpHtvUHJyOnCEFxOlNDtGo7wg==", "dev": true, "license": "BlueOak-1.0.0", "dependencies": { - "@isaacs/cliui": "^8.0.2" + "@isaacs/cliui": "^9.0.0" }, "engines": { "node": "20 || >=22" @@ -11618,31 +11529,15 @@ "license": "MIT" }, "node_modules/workbox-build/node_modules/lru-cache": { - "version": "11.2.4", - "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.4.tgz", - "integrity": "sha512-B5Y16Jr9LB9dHVkh6ZevG+vAbOsNOYCX+sXvFWFu7B3Iz5mijW3zdbMyhsh8ANd2mSWBYdJgnqi+mL7/LrOPYg==", + "version": "11.2.6", + "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.6.tgz", + "integrity": "sha512-ESL2CrkS/2wTPfuend7Zhkzo2u0daGJ/A2VucJOgQ/C48S/zB8MMeMHSGKYpXhIjbPxfuezITkaBH1wqv00DDQ==", "dev": true, "license": "BlueOak-1.0.0", "engines": { "node": "20 || >=22" } }, - "node_modules/workbox-build/node_modules/minimatch": { - "version": "10.1.1", - "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.1.1.tgz", - "integrity": "sha512-enIvLvRAFZYXJzkCYG5RKmPfrFArdLv+R+lbQ53BmIMLIry74bjKzX6iHAm8WYamJkhSSEabrWN5D97XnKObjQ==", - "dev": true, - "license": "BlueOak-1.0.0", - "dependencies": { - "@isaacs/brace-expansion": "^5.0.0" - }, - "engines": { - "node": "20 || >=22" - }, - "funding": { - "url": "https://github.com/sponsors/isaacs" - } - }, "node_modules/workbox-build/node_modules/path-scurry": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/path-scurry/-/path-scurry-2.0.1.tgz", @@ -11741,10 +11636,21 @@ "node": ">=20.0.0" } }, + "node_modules/workbox-cli/node_modules/@isaacs/cliui": { + "version": "9.0.0", + "resolved": "https://registry.npmjs.org/@isaacs/cliui/-/cliui-9.0.0.tgz", + "integrity": "sha512-AokJm4tuBHillT+FpMtxQ60n8ObyXBatq7jD2/JA9dxbDDokKQm8KMht5ibGzLVU9IJDIKK4TPKgMHEYMn3lMg==", + "dev": true, + "license": "BlueOak-1.0.0", + "engines": { + "node": ">=18" + } + }, "node_modules/workbox-cli/node_modules/glob": { "version": "11.1.0", "resolved": "https://registry.npmjs.org/glob/-/glob-11.1.0.tgz", "integrity": "sha512-vuNwKSaKiqm7g0THUBu2x7ckSs3XJLXE+2ssL7/MfTGPLLcrJQ/4Uq1CjPTtO5cCIiRxqvN6Twy1qOwhL0Xjcw==", + "deprecated": "Old versions of glob are not supported, and contain widely publicized security vulnerabilities, which have been fixed in the current version. Please update. Support for old versions may be purchased (at exorbitant rates) by contacting i@izs.me", "dev": true, "license": "BlueOak-1.0.0", "dependencies": { @@ -11766,13 +11672,13 @@ } }, "node_modules/workbox-cli/node_modules/jackspeak": { - "version": "4.1.1", - "resolved": "https://registry.npmjs.org/jackspeak/-/jackspeak-4.1.1.tgz", - "integrity": "sha512-zptv57P3GpL+O0I7VdMJNBZCu+BPHVQUk55Ft8/QCJjTVxrnJHuVuX/0Bl2A6/+2oyR/ZMEuFKwmzqqZ/U5nPQ==", + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/jackspeak/-/jackspeak-4.2.3.tgz", + "integrity": "sha512-ykkVRwrYvFm1nb2AJfKKYPr0emF6IiXDYUaFx4Zn9ZuIH7MrzEZ3sD5RlqGXNRpHtvUHJyOnCEFxOlNDtGo7wg==", "dev": true, "license": "BlueOak-1.0.0", "dependencies": { - "@isaacs/cliui": "^8.0.2" + "@isaacs/cliui": "^9.0.0" }, "engines": { "node": "20 || >=22" @@ -11782,31 +11688,15 @@ } }, "node_modules/workbox-cli/node_modules/lru-cache": { - "version": "11.2.4", - "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.4.tgz", - "integrity": "sha512-B5Y16Jr9LB9dHVkh6ZevG+vAbOsNOYCX+sXvFWFu7B3Iz5mijW3zdbMyhsh8ANd2mSWBYdJgnqi+mL7/LrOPYg==", + "version": "11.2.6", + "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.6.tgz", + "integrity": "sha512-ESL2CrkS/2wTPfuend7Zhkzo2u0daGJ/A2VucJOgQ/C48S/zB8MMeMHSGKYpXhIjbPxfuezITkaBH1wqv00DDQ==", "dev": true, "license": "BlueOak-1.0.0", "engines": { "node": "20 || >=22" } }, - "node_modules/workbox-cli/node_modules/minimatch": { - "version": "10.1.1", - "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.1.1.tgz", - "integrity": "sha512-enIvLvRAFZYXJzkCYG5RKmPfrFArdLv+R+lbQ53BmIMLIry74bjKzX6iHAm8WYamJkhSSEabrWN5D97XnKObjQ==", - "dev": true, - "license": "BlueOak-1.0.0", - "dependencies": { - "@isaacs/brace-expansion": "^5.0.0" - }, - "engines": { - "node": "20 || >=22" - }, - "funding": { - "url": "https://github.com/sponsors/isaacs" - } - }, "node_modules/workbox-cli/node_modules/path-scurry": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/path-scurry/-/path-scurry-2.0.1.tgz", @@ -12068,9 +11958,9 @@ } }, "node_modules/ws": { - "version": "8.18.3", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.3.tgz", - "integrity": "sha512-PEIGCY5tSlUt50cqyMXfCzX+oOPqN0vuGqWzbcJ2xvnkzkq46oOpz7dQaTDBdfICb4N14+GARUDw2XV2N4tvzg==", + "version": "8.19.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.19.0.tgz", + "integrity": "sha512-blAT2mjOEIi0ZzruJfIhb3nps74PRWTCz1IjglWEEpQl5XS/UNama6u2/rjFkDDouqr4L67ry+1aGIALViWjDg==", "dev": true, "license": "MIT", "engines": { diff --git a/package.json b/package.json index 4242cd0..7af8a9e 100644 --- a/package.json +++ b/package.json @@ -54,18 +54,18 @@ "license": "GPL-3.0", "homepage": "https://scigrade.com/", "devDependencies": { - "@playwright/test": "^1.57.0", + "@playwright/test": "^1.58.2", "@types/jest": "^30.0.0", - "@types/node": "^25.0.3", + "@types/node": "^25.2.3", "axe-playwright": "^2.2.2", - "eslint": "^9.39.2", + "eslint": "^10.0.0", "eslint-config-prettier": "^10.1.8", - "eslint-plugin-prettier": "^5.5.4", - "globals": "^17.0.0", + "eslint-plugin-prettier": "^5.5.5", + "globals": "^17.3.0", "http-server": "^14.1.1", "jest": "^30.2.0", "jest-environment-jsdom": "^30.2.0", - "prettier": "^3.7.4", + "prettier": "^3.8.1", "workbox-cli": "^7.4.0" } } From de3b17f26c81d4fa9a6e21c24fd4173c61562d7c Mon Sep 17 00:00:00 2001 From: Alexander Sullivan Date: Wed, 18 Feb 2026 13:33:20 -0500 Subject: [PATCH 2/3] re-ran prettier --- docs/api/index.md | 38 +++---- docs/architecture/index.md | 46 ++++---- docs/guides/data-structures.md | 180 +++++++++++++++---------------- docs/guides/marking-algorithm.md | 97 +++++++++-------- docs/guides/setup.md | 22 ++-- 5 files changed, 194 insertions(+), 189 deletions(-) diff --git a/docs/api/index.md b/docs/api/index.md index f2d9b80..6ac4618 100644 --- a/docs/api/index.md +++ b/docs/api/index.md @@ -136,10 +136,10 @@ function loadWork() - Clears the `#work` HTML element - Sets `loadedMode` to `selection_inMode` - Generates form HTML including: - - Gene background information section - - Input fields for gRNA sequence, PAM, strand, position, off-target score - - Input fields for F1 and R1 primers - - Submit button with `submitAnswers()` handler + - Gene background information section + - Input fields for gRNA sequence, PAM, strand, position, off-target score + - Input fields for F1 and R1 primers + - Submit button with `submitAnswers()` handler **Renders to:** HTML element with ID `work`. @@ -229,10 +229,10 @@ function checkOffTarget(score) - Builds a score list within ±35 positions of the inputted cut position to determine an optimal threshold - Sets `MAROffTarget` and `MAROffTarget_degree` based on the input and calculated thresholds - Degree values: - - `0`: Wrong or below threshold - - `1`: At or above the optimal threshold - - `2`: At or above 35 but below the optimal threshold when the max reference score is at least 80 - - `3`: Only available option when the local max score is below 35 + - `0`: Wrong or below threshold + - `1`: At or above the optimal threshold + - `2`: At or above 35 but below the optimal threshold when the max reference score is at least 80 + - `3`: Only available option when the local max score is below 35 **Used For:** Part of `checkAnswers()` validation. @@ -299,12 +299,12 @@ function markAnswers() - Processes results from `checkAnswers()` - Assigns points for each correct component: - - gRNA sequence - - PAM - - Strand - - Off-target score - - F1 primer - - R1 primer + - gRNA sequence + - PAM + - Strand + - Off-target score + - F1 primer + - R1 primer - Calculates weighted final score **Prerequisite:** `checkAnswers()` must be called first. @@ -435,8 +435,8 @@ The application uses Bootstrap utilities for styling in [core/scripts/crispr_scr ```html
- - + +
@@ -445,9 +445,9 @@ The application uses Bootstrap utilities for styling in [core/scripts/crispr_scr
-
-
-
+
+
+
``` diff --git a/docs/architecture/index.md b/docs/architecture/index.md index 1fcb2b8..06199e0 100644 --- a/docs/architecture/index.md +++ b/docs/architecture/index.md @@ -63,18 +63,18 @@ Structure: ```json { - "gene_list": { - "GENENAME": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] - } + "gene_list": { + "GENENAME": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] + } } ``` @@ -86,17 +86,17 @@ Structure: ```json { - "gene_list": { - "GENENAME": { - "base_type": "practice", - "name": "Gene Full Name", - "Background": "Educational description...", - "Target site": "Nucleotide position X - target description", - "Target position": "123", - "Sequence": "ACGT...", - "NCBI gene link": "https://..." - } - } + "gene_list": { + "GENENAME": { + "base_type": "practice", + "name": "Gene Full Name", + "Background": "Educational description...", + "Target site": "Nucleotide position X - target description", + "Target position": "123", + "Sequence": "ACGT...", + "NCBI gene link": "https://..." + } + } } ``` diff --git a/docs/guides/data-structures.md b/docs/guides/data-structures.md index ae7b8a9..8c42349 100644 --- a/docs/guides/data-structures.md +++ b/docs/guides/data-structures.md @@ -16,12 +16,12 @@ SciGrade uses JSON as its primary data format for gene information and guide RNA ```json { - "_id": "5a67577c01ac2022a0eb6f56", - "owner_id": "5a4cb9e58f25b9cd6d49e868", - "number": 42, - "version": "0.3", - "date": "2018-08-20:1925", - "gene_list": {} + "_id": "5a67577c01ac2022a0eb6f56", + "owner_id": "5a4cb9e58f25b9cd6d49e868", + "number": 42, + "version": "0.3", + "date": "2018-08-20:1925", + "gene_list": {} } ``` @@ -37,17 +37,17 @@ SciGrade uses JSON as its primary data format for gene information and guide RNA ```json { - "gene_list": { - "GENENAME": { - "base_type": "practice", - "name": "Full Gene Name", - "Background": "Educational description...", - "Target site": "Nucleotide position X - description of target", - "Target position": "123", - "Sequence": "ACGTACGT...(full sequence)...ACGT", - "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/12345" - } - } + "gene_list": { + "GENENAME": { + "base_type": "practice", + "name": "Full Gene Name", + "Background": "Educational description...", + "Target site": "Nucleotide position X - description of target", + "Target position": "123", + "Sequence": "ACGTACGT...(full sequence)...ACGT", + "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/12345" + } + } } ``` @@ -69,15 +69,15 @@ From actual data (HBB gene): ```json { - "HBB": { - "base_type": "practice", - "name": "Sickle cell anemia", - "Background": "Sickle cell anaemia is caused by an SNP in the human haemoglobin beta-chain which results in a GAG codon being replaced with a GTG codon (A → T)...", - "Target site": "Nucleotide position 73 - You are trying to change a thymine back to an alanine (WILD-TYPE).", - "Target position": "73", - "Sequence": "ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC", - "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/3043" - } + "HBB": { + "base_type": "practice", + "name": "Sickle cell anemia", + "Background": "Sickle cell anaemia is caused by an SNP in the human haemoglobin beta-chain which results in a GAG codon being replaced with a GTG codon (A → T)...", + "Target site": "Nucleotide position 73 - You are trying to change a thymine back to an alanine (WILD-TYPE).", + "Target position": "73", + "Sequence": "ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC", + "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/3043" + } } ``` @@ -91,12 +91,12 @@ From actual data (HBB gene): ```json { - "_id": "5a8deb6a547dd8319415ac3d", - "owner_id": "5a4cb9e58f25b9cd6d49e868", - "number": 42, - "version": "0.2", - "date": "2018-02-21:1657", - "gene_list": {} + "_id": "5a8deb6a547dd8319415ac3d", + "owner_id": "5a4cb9e58f25b9cd6d49e868", + "number": 42, + "version": "0.2", + "date": "2018-02-21:1657", + "gene_list": {} } ``` @@ -106,18 +106,18 @@ From actual data (HBB gene): ```json { - "gene_list": { - "GENENAME": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] - } + "gene_list": { + "GENENAME": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] + } } ``` @@ -138,24 +138,24 @@ From actual data (HBB gene): ```json { - "HBB": [ - { - "Position": 14, - "Strand": -1, - "Sequence": "AGTGAACACAGTTGTGTCAG", - "PAM": "AAG", - "Specificity Score": 39.0941742, - "Efficiency Score": 10.10900644 - }, - { - "Position": 17, - "Strand": -1, - "Sequence": "GCTAGTGAACACAGTTGTGT", - "PAM": "CAG", - "Specificity Score": 40.4041049, - "Efficiency Score": 22.38758304 - } - ] + "HBB": [ + { + "Position": 14, + "Strand": -1, + "Sequence": "AGTGAACACAGTTGTGTCAG", + "PAM": "AAG", + "Specificity Score": 39.0941742, + "Efficiency Score": 10.10900644 + }, + { + "Position": 17, + "Strand": -1, + "Sequence": "GCTAGTGAACACAGTTGTGT", + "PAM": "CAG", + "Specificity Score": 40.4041049, + "Efficiency Score": 22.38758304 + } + ] } ``` @@ -196,15 +196,15 @@ In [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js): ```javascript async function loadCRISPRJSON_Files() { - try { - const responseBenchling = await fetch("./data/Benchling_gRNA_Outputs.json"); - benchling_gRNA_outputs = await responseBenchling.json(); - - const responseGeneBackground = await fetch("data/Background_info/gene_background_info.json"); - gene_backgroundInfo = await responseGeneBackground.json(); - } catch (err) { - console.error("Error fetching file:", err); - } + try { + const responseBenchling = await fetch("./data/Benchling_gRNA_Outputs.json"); + benchling_gRNA_outputs = await responseBenchling.json(); + + const responseGeneBackground = await fetch("data/Background_info/gene_background_info.json"); + gene_backgroundInfo = await responseGeneBackground.json(); + } catch (err) { + console.error("Error fetching file:", err); + } } ``` @@ -247,15 +247,15 @@ To add a new gene to SciGrade: ```json { - "NEWGENE": { - "base_type": "practice", - "name": "Gene Full Name", - "Background": "Educational description...", - "Target site": "Nucleotide position X - description", - "Target position": "123", - "Sequence": "ACGT... full sequence ...", - "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/..." - } + "NEWGENE": { + "base_type": "practice", + "name": "Gene Full Name", + "Background": "Educational description...", + "Target site": "Nucleotide position X - description", + "Target position": "123", + "Sequence": "ACGT... full sequence ...", + "NCBI gene link": "https://www.ncbi.nlm.nih.gov/gene/..." + } } ``` @@ -263,16 +263,16 @@ To add a new gene to SciGrade: ```json { - "NEWGENE": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] + "NEWGENE": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] } ``` diff --git a/docs/guides/marking-algorithm.md b/docs/guides/marking-algorithm.md index d2842ce..68a28d7 100644 --- a/docs/guides/marking-algorithm.md +++ b/docs/guides/marking-algorithm.md @@ -37,9 +37,9 @@ When a student submits their answer, [checkAnswers()](../../core/scripts/crispr_ ```javascript const inputtedSeq = document.getElementById("sequence_input").value.trim(); for (const answer of benchling_gRNA_outputs.gene_list[current_gene]) { - if (answer.Sequence === inputtedSeq) { - possible_comparable_answers.push(answer); - } + if (answer.Sequence === inputtedSeq) { + possible_comparable_answers.push(answer); + } } ``` @@ -57,27 +57,27 @@ For each possible matching sequence, verify the target nucleotide is within the const correctNucleotidePosition = gene_backgroundInfo.gene_list[current_gene]["Target position"] - 1; if (possibleAnswer.Strand === 1) { - // Sense strand: check if target is within gRNA range - const nucleotideIncludedRange_top = possibleAnswer.Position - 1 - 1 + 3; - const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 17; - - if ( - correctNucleotidePosition >= nucleotideIncludedRange_bot && - correctNucleotidePosition <= nucleotideIncludedRange_top - ) { - correctNucleotideIncluded = true; - } + // Sense strand: check if target is within gRNA range + const nucleotideIncludedRange_top = possibleAnswer.Position - 1 - 1 + 3; + const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 17; + + if ( + correctNucleotidePosition >= nucleotideIncludedRange_bot && + correctNucleotidePosition <= nucleotideIncludedRange_top + ) { + correctNucleotideIncluded = true; + } } else if (possibleAnswer.Strand === -1) { - // Antisense strand: check if target is within gRNA range - const nucleotideIncludedRange_top = possibleAnswer.Position - 1 + 17; - const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 3; - - if ( - correctNucleotidePosition >= nucleotideIncludedRange_bot && - correctNucleotidePosition <= nucleotideIncludedRange_top - ) { - correctNucleotideIncluded = true; - } + // Antisense strand: check if target is within gRNA range + const nucleotideIncludedRange_top = possibleAnswer.Position - 1 + 17; + const nucleotideIncludedRange_bot = possibleAnswer.Position - 1 - 3; + + if ( + correctNucleotidePosition >= nucleotideIncludedRange_bot && + correctNucleotidePosition <= nucleotideIncludedRange_top + ) { + correctNucleotideIncluded = true; + } } ``` @@ -91,13 +91,13 @@ Check if the student selected the correct strand: ```javascript if (possibleAnswer.Strand === 1) { - if (document.getElementById("strand_input").value === "Sense (+)") { - MARstrand = true; - } + if (document.getElementById("strand_input").value === "Sense (+)") { + MARstrand = true; + } } else if (possibleAnswer.Strand === -1) { - if (document.getElementById("strand_input").value === "Antisense (-)") { - MARstrand = true; - } + if (document.getElementById("strand_input").value === "Antisense (-)") { + MARstrand = true; + } } ``` @@ -107,14 +107,15 @@ if (possibleAnswer.Strand === 1) { - Strand `-1` = Antisense (-) strand ### Step 5: PAM Sequence Validation + PAM validation compares the student's input to the `PAM` value on the matched reference entry in [core/data/Benchling_gRNA_Outputs.json](../../core/data/Benchling_gRNA_Outputs.json) as implemented in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ### Step 6: Off-Target Score Validation ```javascript function checkOffTarget(score) { - // Check if off-target score meets minimum threshold - // Threshold depends on marking mode settings + // Check if off-target score meets minimum threshold + // Threshold depends on marking mode settings } ``` @@ -136,9 +137,11 @@ The off-target score uses the following steps in [core/scripts/crispr_scripts.js ### Step 7: Primer Validation #### F1 Primer Check + The F1 primer is validated by building candidate primers with the `TAATACGACTCACTATAG` prefix and the first 16-20 bases of the submitted gRNA sequence in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). #### R1 Primer Check + The R1 primer is validated by building a reverse-complement string and then constructing candidate primers with the `TTCTAGCTCTAAAAC` prefix and the first 19-20 bases of the reverse complement in [core/scripts/crispr_scripts.js](../../core/scripts/crispr_scripts.js). ## Scoring Logic @@ -202,12 +205,14 @@ sequenceDiagram In account management modal (opened via [openAccountManagement()](../../core/scripts/crispr_scripts.js#L853)): 1. Select "Optimal" mode: - - Calculates `Min_optimal = Max_range - (Max_range * 0.2)` from nearby scores - - Uses 80 as the threshold when `Min_optimal` is greater than 80 or less than 35 + +- Calculates `Min_optimal = Max_range - (Max_range * 0.2)` from nearby scores +- Uses 80 as the threshold when `Min_optimal` is greater than 80 or less than 35 2. Select "Custom" mode: - Enter specific value (0.01 - 100) - - Stored in `student_reg_information[0].classMarkingMod` for the selected class + +- Stored in `student_reg_information[0].classMarkingMod` for the selected class ### Adding Custom Marking Rules @@ -224,18 +229,18 @@ Ensure reference data in [Benchling_gRNA_Outputs.json](../../core/data/Benchling ```json { - "gene_list": { - "GENENAME": [ - { - "Position": 123, - "Strand": 1, - "Sequence": "ACGTACGTACGTACGTACGT", - "PAM": "NGG", - "Specificity Score": 45.2, - "Efficiency Score": 78.5 - } - ] - } + "gene_list": { + "GENENAME": [ + { + "Position": 123, + "Strand": 1, + "Sequence": "ACGTACGTACGTACGTACGT", + "PAM": "NGG", + "Specificity Score": 45.2, + "Efficiency Score": 78.5 + } + ] + } } ``` diff --git a/docs/guides/setup.md b/docs/guides/setup.md index 2147280..11f56f2 100644 --- a/docs/guides/setup.md +++ b/docs/guides/setup.md @@ -95,17 +95,17 @@ Structure: ```json { - "gene_list": { - "GENENAME": { - "base_type": "practice|assignment", - "name": "Full Gene Name", - "Background": "Description of gene and mutation", - "Target site": "Location and nature of target", - "Target position": "Numeric position", - "Sequence": "ACGT... full DNA sequence", - "NCBI gene link": "https://..." - } - } + "gene_list": { + "GENENAME": { + "base_type": "practice|assignment", + "name": "Full Gene Name", + "Background": "Description of gene and mutation", + "Target site": "Location and nature of target", + "Target position": "Numeric position", + "Sequence": "ACGT... full DNA sequence", + "NCBI gene link": "https://..." + } + } } ``` From c27297356f1b2f5d9e1e9c29d246f886ee968552 Mon Sep 17 00:00:00 2001 From: Alexander Sullivan Date: Wed, 18 Feb 2026 13:35:49 -0500 Subject: [PATCH 3/3] update jQuery --- core/scripts/APIandLibraries/jQuery/jquery.min.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/scripts/APIandLibraries/jQuery/jquery.min.js 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