-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
10 changed files
with
986 additions
and
16 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| <?xml version="1.0" encoding="utf-8"?> | ||
| <django-objects version="1.0"> | ||
| <object pk="1" model="backend.Course"> | ||
| <field name="code">C1</field> | ||
| <field name="owner">1</field> | ||
| <field name="administrators">1</field> | ||
| <field name="students">1</field> | ||
| <field name="status">2</field> | ||
| </object> | ||
|
|
||
| </django-objects> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,379 @@ | ||
| <xml><![CDATA[ { | ||
| id: 'assignment_2', | ||
| course: '7.02', | ||
| name: '7.02 StarCellBio Prototype Assignment', | ||
| description: 'Biochemical approach to analyzing vulva development in <i>C. elegans.</i>', | ||
| experiments: { | ||
| }, | ||
| template: { | ||
| instructions: 'Your new lab is studying vulva development in <i>C. elegans</i>. You screen a chemical library and identify four new drugs, which all affect vulva development, and you name them Vulvarine 1, 2, 3 and 4.<br><br>Increasing amounts of Vulvarines 1 and 2 result in a vulvaless phenotype in the wild-type worms whereas treatment of wild-type worms with Vulvarines 3 and 4 results in a multivulva phenotype. Your advisor tells you that some proteins involved in the vulva development pathway are already known and she advises you to do western blots to test if some of these proteins are affected by these treatments.<br><br>i) Use the StarCellBio software to analyze the western blots from worms treated with increasing doses of Vulvarines. Choose the gene products whose expression you would like to check. <br>ii) Which proteins are affected by Vulvarine treatment? What is the critical Vulvarine concentration for each treatment?<br> iii) Look up the biological function of each protein whose expression is affected by the drug and speculate as to how the change in its levels may have a role in vulva development.<br>', | ||
| add_new_row_instructions: 'On this page, set up your experiment to treat the wild-type worms with the four new drugs, Vulvarines 1-4, identified in your chemical screen. <ul><li>To get started, click <b>Add Treatment Protocol.</b></li><li>For each treatment protocol, select the <i>C. elegans</i> strain, treatment(s), and treatment dose.</li><li> For all of your treatments, treat the <i>C. elegans</i> immediately (time = 0 minutes) and collect after 3 days.</li><li>Once you finish setting up your experiment, select <b>Finish setup & run experiment.</b> After you run your experiment, you will be unable to change your treatment protocols.</li></ul>', | ||
| ui_configuration: { | ||
| experiment_steps_setup: true, // this is not even checked... | ||
| experiment_steps_western_blot: true, | ||
| experiment_steps_facs: false, | ||
| experiment_steps_microscopy: false, | ||
| treatment_options_display_temperature: false, | ||
| treatment_options_edit_schedule: false, | ||
| lysate_display_ip: false, | ||
| amount_of_protein_loaded: 50, | ||
| experiment_setup_duration: 3600, // seconds | ||
| experiment_setup_resolution_height: 3600, | ||
| experiment_setup_physical_height: 600, | ||
| collection_times_fixed: true, | ||
| maximum_number_of_treatments_per_protocol: 1, | ||
| show_add_new_experiment_rows: true | ||
| }, | ||
| drug_template: { | ||
| name: 'Buffer only', | ||
| drug_id: 'nc', | ||
| concentration_id: 0 | ||
| }, | ||
| experiment_templates: { | ||
| 'default': { | ||
| collection_schedule_list: { | ||
| list: [ | ||
| { | ||
| schedule: "3 d", | ||
| schedule_value: 3600 * 24 * 3, | ||
| id: '3 d' | ||
| } | ||
| ] | ||
| }, | ||
| treatment: { | ||
| schedule_value: 0, | ||
| schedule: 'immediately', | ||
| duration_value: 3600 * 24 * 3, | ||
| duration: '3 d' | ||
| } | ||
| }, | ||
| 'treatment_protocol_template': { | ||
| 'P1': { | ||
| title: 'Basic protocol', | ||
| treatment_list: { | ||
| list: [ | ||
| {schedule_value: 0, schedule: 'immediately', duration_value: 3600 * 24 * 3, duration: '3 d', drug_list: {list: [ | ||
| {drug_id: 'nc', concentration_id: 0} | ||
| ]}} | ||
| ] | ||
| }, | ||
| collection_schedule_list: { | ||
| list: [ | ||
| { | ||
| schedule: "3 d", | ||
| schedule_value: 3600 * 24 * 3, | ||
| id: '3 d' | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| name: '7.02 StarCellBio Prototype Assignment', | ||
| concentrations: { | ||
| 1: { | ||
| name: '1 ' + microEntity + 'M', | ||
| value: 1000 | ||
| }, | ||
| 5: { | ||
| name: '5 ' + microEntity + 'M', | ||
| value: 5000 | ||
| }, | ||
| 10: { | ||
| name: '10 ' + microEntity + 'M', | ||
| value: 10000 | ||
| }, | ||
| 20: { | ||
| name: '20 ' + microEntity + 'M', | ||
| value: 20000 | ||
| }, | ||
| 25: { | ||
| name: '25 ' + microEntity + 'M', | ||
| value: 25000 | ||
| }, | ||
| 40: { | ||
| name: '40 ' + microEntity + 'M', | ||
| value: 40000 | ||
| }, | ||
| 80: { | ||
| name: '80 ' + microEntity + 'M', | ||
| value: 80000 | ||
| }, | ||
| 125: { | ||
| name: '125 ' + microEntity + 'M', | ||
| value: 125000 | ||
| }, | ||
| '10n': { | ||
| name: '10 nM', | ||
| value: 10 | ||
| }, | ||
| 50: { | ||
| name: '50 nM', | ||
| value: 50 | ||
| }, | ||
| 100: { | ||
| name: '100 nM', | ||
| value: 100 | ||
| }, | ||
| 200: { | ||
| name: '200 nM', | ||
| value: 200 | ||
| }, | ||
| 400: { | ||
| name: '400 nM', | ||
| value: 400 | ||
| }, | ||
| 0: { | ||
| name: '0 nM', | ||
| value: 0 | ||
| } | ||
| }, | ||
| drugs: { | ||
| 'nc': { | ||
| name: 'Buffer only', | ||
| concentrations: [0] | ||
| }, | ||
| 1: { | ||
| name: 'Vulvarine 1', | ||
| concentrations: [5, 10, 20, 40, 80] | ||
| }, | ||
| 2: { | ||
| name: 'Vulvarine 2', | ||
| concentrations: [50, 100, 200, 400] | ||
| }, | ||
| 3: { | ||
| name: 'Vulvarine 3', | ||
| concentrations: [1, 5, 25, 125] | ||
| }, | ||
| 4: { | ||
| name: 'Vulvarine 4', | ||
| concentrations: ['10n', 50, 100, 200, 400] | ||
| } | ||
| }, | ||
| experiment_temperatures: { | ||
| '25': { | ||
| name: "25" + degreeEntity + "C" | ||
| } | ||
| }, | ||
| cell_lines: { | ||
| 'wt': { | ||
| name: 'Wild Type' | ||
| } | ||
|
|
||
| }, | ||
| time_unit: { | ||
| kind: 'minutes' | ||
| }, | ||
| primary_anti_body: { | ||
| 1: { | ||
| name: 'rabbit anti-let-23', | ||
| secondary: [1], | ||
| marks: [ | ||
| {weight: 24, intensity: .11}, | ||
| {weight: 36, intensity: .4}, | ||
| {weight: 48, intensity: .04} | ||
| ] | ||
| }, | ||
| 2: { | ||
| name: 'mouse anti-let-60', | ||
| secondary: [3], | ||
| marks: [ | ||
| {weight: 48, intensity: .04} | ||
| ] | ||
| }, | ||
| 3: { | ||
| name: 'goat anti-lin15A', | ||
| secondary: [2], | ||
| marks: [ | ||
| {weight: 12, intensity: .02} | ||
| ] | ||
| }, | ||
| 9: { | ||
| name: 'goat anti-lin15B', | ||
| secondary: [2], | ||
| marks: [ | ||
| {weight: 100, intensity: .01}, | ||
| {weight: 129, intensity: .11} | ||
| ] | ||
| }, | ||
| 4: { | ||
| name: 'goat anti-lin-1', | ||
| secondary: [2] | ||
| }, | ||
| 5: { | ||
| name: 'mouse anti-Dpy-5', | ||
| secondary: [3] | ||
| }, | ||
| 6: { | ||
| name: 'rabbit anti-Lon-2', | ||
| secondary: [1] | ||
| }, | ||
| 7: { | ||
| name: 'mouse anti-Sma-4', | ||
| secondary: [3] | ||
| }, | ||
| 8: { | ||
| name: 'goat anti-Unc-22', | ||
| secondary: [2] | ||
| } | ||
| }, | ||
| secondary_anti_body: { | ||
| 1: { | ||
| name: 'donkey anti-rabbit' | ||
| }, | ||
| 2: { | ||
| name: 'rabbit anti-goat' | ||
| }, | ||
| 3: { | ||
| name: 'goat anti-mouse' | ||
| } | ||
| }, | ||
| lysate_kinds: { | ||
| 'whole': { | ||
| name: 'Whole Cell' | ||
| }, | ||
| 'cyto': { | ||
| name: 'Cytoplasm' | ||
| }, | ||
| 'nuclear': { | ||
| name: 'Nuclear' | ||
| } | ||
| }, | ||
| model: {// model | ||
| western_blot: {// this applies to western blot | ||
| 'cyto': {// it acts on cytoplasm (thus on whole cell lysate as well) | ||
| 'parser_fixed': [ | ||
| { | ||
| 'cell_line': 'wt', | ||
| 'transfer_function': 'delta', | ||
| 'drug': 1, // Vul 1 | ||
| 'cutoff': 10000, | ||
| 'above_marks': [ | ||
| { | ||
| name: 'let-23', | ||
| weight: 150, | ||
| intensity: -40, | ||
| primary_anti_body: [1] | ||
| } | ||
| ], | ||
| 'below_marks': [] | ||
| }, | ||
| { | ||
| 'cell_line': 'wt', | ||
| 'transfer_function': 'delta', | ||
| 'drug': 2, // Vul 2 | ||
| 'cutoff': 200, | ||
| 'above_marks': [ | ||
| { | ||
| name: 'let-60', | ||
| weight: 21, | ||
| intensity: -100, | ||
| primary_anti_body: [2] | ||
| } | ||
| ], | ||
| 'below_marks': [] | ||
| }, | ||
| { | ||
| 'cell_line': 'wt', | ||
| 'transfer_function': 'delta', | ||
| 'drug': 3, // Vul 3 | ||
| 'cutoff': 25000, | ||
| 'above_marks': [ | ||
| { | ||
| name: 'let-15A', | ||
| weight: 79, | ||
| intensity: -100, | ||
| primary_anti_body: [3] | ||
| }, | ||
| { | ||
| name: 'let-15B', | ||
| weight: 163, | ||
| intensity: -100, | ||
| primary_anti_body: [9] | ||
|
|
||
| } | ||
| ], | ||
| 'below_marks': [] | ||
| }, | ||
| { | ||
| 'cell_line': 'wt', | ||
| 'transfer_function': 'delta', | ||
| 'drug': 4, // Vul 3 | ||
| 'cutoff': 400, | ||
| 'above_marks': [ | ||
| { | ||
| name: 'let-1', | ||
| weight: 48, | ||
| intensity: -100, | ||
| primary_anti_body: [4] | ||
| } | ||
| ], | ||
| 'below_marks': [] | ||
| }, | ||
| { | ||
| 'cell_line': 'wt', | ||
| 'transfer_function': 'static', | ||
| 'marks': [ | ||
| { | ||
| name: 'let-23', | ||
| weight: 150, | ||
| intensity: 40, | ||
| primary_anti_body: [1] | ||
| }, | ||
| { | ||
| name: 'let-60', | ||
| weight: 21, | ||
| intensity: 100, | ||
| primary_anti_body: [2] | ||
| }, | ||
| { | ||
| name: 'let-15A', | ||
| weight: 79, | ||
| intensity: 100, | ||
| primary_anti_body: [3] | ||
| }, | ||
| { | ||
| name: 'let-15B', | ||
| weight: 163, | ||
| intensity: 100, | ||
| primary_anti_body: [9] | ||
| }, | ||
| { | ||
| name: 'let-1', | ||
| weight: 48, | ||
| intensity: 100, | ||
| primary_anti_body: [4] | ||
| }, | ||
| { | ||
| name: 'Dpy-5', | ||
| weight: 20, | ||
| intensity: 60, | ||
| primary_anti_body: [5] | ||
| }, | ||
| { | ||
| name: 'Lan-2', | ||
| weight: 100, | ||
| intensity: 40, | ||
| primary_anti_body: [6] | ||
| }, | ||
| { | ||
| name: 'Sma-4', | ||
| weight: 75, | ||
| intensity: 25, | ||
| primary_anti_body: [7] | ||
| }, | ||
| { | ||
| name: 'Unc-22', | ||
| weight: 40, | ||
| intensity: 10, | ||
| primary_anti_body: [8] | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } ]]> | ||
| </xml> |
Oops, something went wrong.