Skip to content

Commit 248eb74

Browse files
seohyonkimseohyonkim
authored
modify remaining quizzes (#341)
1 parent 30cf0a7 commit 248eb74

File tree

2 files changed

+278
-43
lines changed

2 files changed

+278
-43
lines changed

‎jupyter-book/air_repertoire/multimodal_integration.ipynb‎

Lines changed: 277 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -2384,25 +2384,282 @@
23842384
"id": "54051eba",
23852385
"metadata": {},
23862386
"source": [
2387-
"## Questions\n",
2388-
"\n",
2389-
"Why could it be useful to integrate AIR sequence information with gene expression?\n",
2390-
"- GEX can be used to improve AIR sequence reads.\n",
2391-
"- \\+ Both modalities provide different insights into the cell, while still being interdependent.\n",
2392-
"- Since both modalities capture the same information, integrating them provides an additional quality check.\n",
2393-
"- For most cells either GEX or AIR is measured. Integrating thereby allows analysis of all cells.\n",
2394-
"\n",
2395-
"What information provides us the AIR sequence, that is not directly captured in GEX?\n",
2396-
"- A count matrix between cells and antibody-tagged epitope bindings.\n",
2397-
"- The IR sequence can be used for demultiplexing between different donors.\n",
2398-
"- \\+ The cell's clonotype and, thereby, cell ancestry is defined by the AIR sequence.\n",
2399-
"- \\+ The AIR sequence determines specificity and is therefor a barcode for recognizing the same epitope.\n",
2387+
"## Quiz"
2388+
]
2389+
},
2390+
{
2391+
"cell_type": "code",
2392+
"execution_count": 2,
2393+
"id": "790b3916",
2394+
"metadata": {
2395+
"tags": [
2396+
"remove_input"
2397+
]
2398+
},
2399+
"outputs": [
2400+
{
2401+
"data": {
2402+
"text/html": [
2403+
"\n",
2404+
" <style>\n",
2405+
" div#flip-card .output.text_html {\n",
2406+
" background-color: transparent;\n",
2407+
" }\n",
2408+
" .flip-card-q1 {\n",
2409+
" background-color: transparent;\n",
2410+
" width: 350px;\n",
2411+
" height: 200px;\n",
2412+
" perspective: 1000px;\n",
2413+
" display: inline-block;\n",
2414+
" margin: 10px;\n",
2415+
" text-align: center;\n",
2416+
" padding: 10px;\n",
2417+
" }\n",
2418+
" .flip-card-inner-q1 {\n",
2419+
" position: relative;\n",
2420+
" width: 100%;\n",
2421+
" height: 100%;\n",
2422+
" text-align: center;\n",
2423+
" transition: transform 0.6s;\n",
2424+
" transform-style: preserve-3d;\n",
2425+
" transform-origin: center;\n",
2426+
" }\n",
2427+
" .flip-card-q1:hover .flip-card-inner-q1 {\n",
2428+
" transform: rotateY(180deg);\n",
2429+
" }\n",
2430+
" .flip-card-front-q1, .flip-card-back-q1 {\n",
2431+
" position: absolute;\n",
2432+
" width: 100%;\n",
2433+
" height: 100%;\n",
2434+
" min-height: 200px;\n",
2435+
" backface-visibility: hidden;\n",
2436+
" display: flex;\n",
2437+
" align-items: center;\n",
2438+
" justify-content: center;\n",
2439+
" font-weight: bold;\n",
2440+
" color: white;\n",
2441+
" padding: 20px;\n",
2442+
" border-radius: 15px;\n",
2443+
" box-sizing: border-box;\n",
2444+
" overflow: hidden;\n",
2445+
" text-align: center;\n",
2446+
" }\n",
2447+
" .flip-card-front-q1 {\n",
2448+
" background-color: #3965a3;\n",
2449+
" font-size: 20px;\n",
2450+
" }\n",
2451+
" .flip-card-back-q1 {\n",
2452+
" background-color: #a8d480;\n",
2453+
" transform: rotateY(180deg);\n",
2454+
" font-size: 20px;\n",
2455+
" }\n",
2456+
" </style>\n",
2457+
"\n",
2458+
" <div class=\"flip-card-q1\">\n",
2459+
" <div class=\"flip-card-inner-q1\">\n",
2460+
" <div class=\"flip-card-front-q1\">\n",
2461+
" Why could it be useful to integrate AIR sequence information with gene expression?\n",
2462+
" </div>\n",
2463+
" <div class=\"flip-card-back-q1\">\n",
2464+
" GEX can be used to improve AIR sequence reads, both modalities provide different insights into the cell, while still being interdependent, etc.\n",
2465+
" </div>\n",
2466+
" </div>\n",
2467+
" </div>\n",
2468+
" <noscript>\n",
2469+
" <p><strong>Q:</strong> Why could it be useful to integrate AIR sequence information with gene expression?</p>\n",
2470+
" <p><strong>Answer:</strong> GEX can be used to improve AIR sequence reads, both modalities provide different insights into the cell, while still being interdependent, etc.</p>\n",
2471+
" </noscript>\n",
2472+
" "
2473+
],
2474+
"text/plain": [
2475+
"<IPython.core.display.HTML object>"
2476+
]
2477+
},
2478+
"metadata": {},
2479+
"output_type": "display_data"
2480+
},
2481+
{
2482+
"data": {
2483+
"text/html": [
2484+
"\n",
2485+
" <style>\n",
2486+
" div#flip-card .output.text_html {\n",
2487+
" background-color: transparent;\n",
2488+
" }\n",
2489+
" .flip-card-q2 {\n",
2490+
" background-color: transparent;\n",
2491+
" width: 350px;\n",
2492+
" height: 200px;\n",
2493+
" perspective: 1000px;\n",
2494+
" display: inline-block;\n",
2495+
" margin: 10px;\n",
2496+
" text-align: center;\n",
2497+
" padding: 10px;\n",
2498+
" }\n",
2499+
" .flip-card-inner-q2 {\n",
2500+
" position: relative;\n",
2501+
" width: 100%;\n",
2502+
" height: 100%;\n",
2503+
" text-align: center;\n",
2504+
" transition: transform 0.6s;\n",
2505+
" transform-style: preserve-3d;\n",
2506+
" transform-origin: center;\n",
2507+
" }\n",
2508+
" .flip-card-q2:hover .flip-card-inner-q2 {\n",
2509+
" transform: rotateY(180deg);\n",
2510+
" }\n",
2511+
" .flip-card-front-q2, .flip-card-back-q2 {\n",
2512+
" position: absolute;\n",
2513+
" width: 100%;\n",
2514+
" height: 100%;\n",
2515+
" min-height: 200px;\n",
2516+
" backface-visibility: hidden;\n",
2517+
" display: flex;\n",
2518+
" align-items: center;\n",
2519+
" justify-content: center;\n",
2520+
" font-weight: bold;\n",
2521+
" color: white;\n",
2522+
" padding: 20px;\n",
2523+
" border-radius: 15px;\n",
2524+
" box-sizing: border-box;\n",
2525+
" overflow: hidden;\n",
2526+
" text-align: center;\n",
2527+
" }\n",
2528+
" .flip-card-front-q2 {\n",
2529+
" background-color: #3965a3;\n",
2530+
" font-size: 20px;\n",
2531+
" }\n",
2532+
" .flip-card-back-q2 {\n",
2533+
" background-color: #a8d480;\n",
2534+
" transform: rotateY(180deg);\n",
2535+
" font-size: 20px;\n",
2536+
" }\n",
2537+
" </style>\n",
2538+
"\n",
2539+
" <div class=\"flip-card-q2\">\n",
2540+
" <div class=\"flip-card-inner-q2\">\n",
2541+
" <div class=\"flip-card-front-q2\">\n",
2542+
" What information provides us the AIR sequence, that is not directly captured in GEX?\n",
2543+
" </div>\n",
2544+
" <div class=\"flip-card-back-q2\">\n",
2545+
" A count matrix between cells and antibody-tagged epitope bindings, the IR sequence can be used for demultiplexing between different donors, etc.\n",
2546+
" </div>\n",
2547+
" </div>\n",
2548+
" </div>\n",
2549+
" <noscript>\n",
2550+
" <p><strong>Q:</strong> What information provides us the AIR sequence, that is not directly captured in GEX?</p>\n",
2551+
" <p><strong>Answer:</strong> A count matrix between cells and antibody-tagged epitope bindings, the IR sequence can be used for demultiplexing between different donors, etc.</p>\n",
2552+
" </noscript>\n",
2553+
" "
2554+
],
2555+
"text/plain": [
2556+
"<IPython.core.display.HTML object>"
2557+
]
2558+
},
2559+
"metadata": {},
2560+
"output_type": "display_data"
2561+
},
2562+
{
2563+
"data": {
2564+
"text/html": [
2565+
"\n",
2566+
" <style>\n",
2567+
" div#flip-card .output.text_html {\n",
2568+
" background-color: transparent;\n",
2569+
" }\n",
2570+
" .flip-card-q3 {\n",
2571+
" background-color: transparent;\n",
2572+
" width: 350px;\n",
2573+
" height: 200px;\n",
2574+
" perspective: 1000px;\n",
2575+
" display: inline-block;\n",
2576+
" margin: 10px;\n",
2577+
" text-align: center;\n",
2578+
" padding: 10px;\n",
2579+
" }\n",
2580+
" .flip-card-inner-q3 {\n",
2581+
" position: relative;\n",
2582+
" width: 100%;\n",
2583+
" height: 100%;\n",
2584+
" text-align: center;\n",
2585+
" transition: transform 0.6s;\n",
2586+
" transform-style: preserve-3d;\n",
2587+
" transform-origin: center;\n",
2588+
" }\n",
2589+
" .flip-card-q3:hover .flip-card-inner-q3 {\n",
2590+
" transform: rotateY(180deg);\n",
2591+
" }\n",
2592+
" .flip-card-front-q3, .flip-card-back-q3 {\n",
2593+
" position: absolute;\n",
2594+
" width: 100%;\n",
2595+
" height: 100%;\n",
2596+
" min-height: 200px;\n",
2597+
" backface-visibility: hidden;\n",
2598+
" display: flex;\n",
2599+
" align-items: center;\n",
2600+
" justify-content: center;\n",
2601+
" font-weight: bold;\n",
2602+
" color: white;\n",
2603+
" padding: 20px;\n",
2604+
" border-radius: 15px;\n",
2605+
" box-sizing: border-box;\n",
2606+
" overflow: hidden;\n",
2607+
" text-align: center;\n",
2608+
" }\n",
2609+
" .flip-card-front-q3 {\n",
2610+
" background-color: #3965a3;\n",
2611+
" font-size: 20px;\n",
2612+
" }\n",
2613+
" .flip-card-back-q3 {\n",
2614+
" background-color: #a8d480;\n",
2615+
" transform: rotateY(180deg);\n",
2616+
" font-size: 15px;\n",
2617+
" }\n",
2618+
" </style>\n",
2619+
"\n",
2620+
" <div class=\"flip-card-q3\">\n",
2621+
" <div class=\"flip-card-inner-q3\">\n",
2622+
" <div class=\"flip-card-front-q3\">\n",
2623+
" On what premise rely multi-modal integration approaches?\n",
2624+
" </div>\n",
2625+
" <div class=\"flip-card-back-q3\">\n",
2626+
" Cells of same or alike AIRs often have a similar phenotype, information of AIR and GEX provide orthogonal information to each other, since they are independent, etc.\n",
2627+
" </div>\n",
2628+
" </div>\n",
2629+
" </div>\n",
2630+
" <noscript>\n",
2631+
" <p><strong>Q:</strong> On what premise rely multi-modal integration approaches?</p>\n",
2632+
" <p><strong>Answer:</strong> Cells of same or alike AIRs often have a similar phenotype, information of AIR and GEX provide orthogonal information to each other, since they are independent, etc.</p>\n",
2633+
" </noscript>\n",
2634+
" "
2635+
],
2636+
"text/plain": [
2637+
"<IPython.core.display.HTML object>"
2638+
]
2639+
},
2640+
"metadata": {},
2641+
"output_type": "display_data"
2642+
}
2643+
],
2644+
"source": [
2645+
"%run ../src/lib.py\n",
24002646
"\n",
2401-
"On what premise rely multi-modal integration approaches?\n",
2402-
"- \\+ Cells of same or alike AIRs often have a similar phenotype.\n",
2403-
"- Information of AIR and GEX provide orthogonal information to each other, since they are independent.\n",
2404-
"- Knowledge is transferred between large gene expression datasets into which AIR data can be mapped.\n",
2405-
"- Each cell occurs clonally expanded and thereby provides multiple gene profiles."
2647+
"flip_card(\n",
2648+
" \"q1\",\n",
2649+
" \"Why could it be useful to integrate AIR sequence information with gene expression?\",\n",
2650+
" \"GEX can be used to improve AIR sequence reads, both modalities provide different insights into the cell, while still being interdependent, etc.\",\n",
2651+
")\n",
2652+
"flip_card(\n",
2653+
" \"q2\",\n",
2654+
" \"What information provides us the AIR sequence, that is not directly captured in GEX?\",\n",
2655+
" \"A count matrix between cells and antibody-tagged epitope bindings, the IR sequence can be used for demultiplexing between different donors, etc.\",\n",
2656+
")\n",
2657+
"flip_card(\n",
2658+
" \"q3\",\n",
2659+
" \"On what premise rely multi-modal integration approaches?\",\n",
2660+
" \"Cells of same or alike AIRs often have a similar phenotype, information of AIR and GEX provide orthogonal information to each other, since they are independent, etc.\",\n",
2661+
" back_font_size=15,\n",
2662+
")"
24062663
]
24072664
},
24082665
{
@@ -2426,7 +2683,7 @@
24262683
],
24272684
"metadata": {
24282685
"kernelspec": {
2429-
"display_name": "Python 3",
2686+
"display_name": "book",
24302687
"language": "python",
24312688
"name": "python3"
24322689
},
@@ -2440,12 +2697,7 @@
24402697
"name": "python",
24412698
"nbconvert_exporter": "python",
24422699
"pygments_lexer": "ipython3",
2443-
"version": "3.11.5"
2444-
},
2445-
"vscode": {
2446-
"interpreter": {
2447-
"hash": "e7370f93d1d0cde622a1f8e1c04877d8463912d04d973331ad4851f04de6915a"
2448-
}
2700+
"version": "3.11.8"
24492701
}
24502702
},
24512703
"nbformat": 4,

‎jupyter-book/air_repertoire/specificity.ipynb‎

Lines changed: 1 addition & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -3208,24 +3208,7 @@
32083208
"id": "1c0380ea",
32093209
"metadata": {},
32103210
"source": [
3211-
"## Quiz\n",
3212-
"What is assumed to be the most important AIR information, when considering specificity?\n",
3213-
"- \\+ CDR3 of the VDJ-chain\n",
3214-
"- V-, and J-gene of the VJ-chain\n",
3215-
"- The constant region\n",
3216-
"- Charge of the CDR2\n",
3217-
"\n",
3218-
"How can you computational infer specificity of AIR cells?\n",
3219-
"- Transforming the epitope Sequence to CDR3-format\n",
3220-
"- \\+ Querying appropriate databases\n",
3221-
"- \\+ Via prediction tools\n",
3222-
"- \\+ By comparing the AIR sequence with known binders\n",
3223-
"\n",
3224-
"Why should you be careful when using database queries?\n",
3225-
"- Most databases only include low-throughput samples.\n",
3226-
"- \\+ Databases are biased toward well researched diseases or epitopes.\n",
3227-
"- Epitopes from databases are often not relevant to actual research.\n",
3228-
"- \\+ Databases might follow different sequence definition and formatting."
3211+
"## Quiz"
32293212
]
32303213
},
32313214
{

0 commit comments

Comments
 (0)