Website for VCellDB.org

[vcellmike]

Background

VCell (http://vcell.org/; https://github.com/virtualcell/vcell) is an open-source software platform that can model and simulate reaction networks. It is in existence for over 20 years and has several thousand users. It is a client-based architecture with models centrally stored in Oracle database. The models can be accessed via REST API https://vcell.cam.uchc.edu/api/v0/biomodel. The prototype interface for accessing and displaying model information is deployed at http://www.vcelldb.org (currently maybe working improperly), available at https://github.com/virtualcell/modelbricks-webapp. It is implemented in Handlebars, with most information retrieved via API, and some information stored locally as JSON.

Goal

1. Provide a complete search and filter page.
2. Add static pages as directed.
3. Redesign and add missing elements to model pages.
4. Make all pages scalable and pretty.
5. Use visualization as implemented in https://bnglviz.github.io/examples.html (https://github.com/bnglViz/bnglViz.github.io)
6. Modify REST API to add retrieval of new elements.

Difficulty Level: Easy/Medium

Provided good skills in HTML/CSS, Handlebars and Java skills to update API, the project is very technical and visual.

Size and Length of Project

• medium: 175 hours
• 12 weeks

Skills

Essential skills: Handlebars, Javascript, CSS, HTML
Desired: Java, REST API

Public Repository

https://github.com/virtualcell/modelbricks-webapp

Potential Mentors

Michael Blinov
James Schaff

[adilkadivala]

Hi @vcellmike , i'm Adil kadival, really excite to work on this project

[vcellmike]

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. *** Hi Adil, Your GitHub looks impressive. I explored some of your projects. I successfully ran https://github.com/adilkadivala/adminDashboard, and it looks great, although I didn't figure out what it does 😉 I tried to run https://github.com/adilkadivala/ai_project, but got an error Server Error Error: @clerk/nextjs: Missing publishableKey. You can get your key at https://dashboard.clerk.com/last-active?path=api-keys. This error happened while generating the page. Any console logs will be displayed in the terminal window. Source <unknown> file:///Users/mblinov/Software/ai_project/node_modules/%20(clerk/nextjs/dist/esm/utils/debugLogger.js (51) middleware.ts (3:32) @ eval 1 | import { clerkMiddleware, createRouteMatcher } from ***@***.***/nextjs/server"; 2 |

3 | export default clerkMiddleware((auth, req) => {

| ^ 4 | if (isProtectedRoute(req)) auth().protect(); 5 | }); 6 | ./middleware.ts file:///Users/mblinov/Software/ai_project/.next/server/middleware.js (50:1) __webpack_require__ file:///Users/mblinov/Software/ai_project/.next/server/edge-runtime-webpack.js (37:33) fn file:///Users/mblinov/Software/ai_project/.next/server/edge-runtime-webpack.js (273:21) Can you please update README so everyone running it will have no issues. I'm not familiar with https://dashboard.clerk.com/, so some words in README on how to proceed will help. Before I start digging into this one, can you please point me to 1-2 other projects in your GitHub that I can easily run? finance got the same Error: @clerk/nextjs: Missing publishableKey. You can get your key at https://dashboard.clerk.com/last-active?path=api-keys. Other pinned projects need dependencies that will take time to set up. Also, are you familiar with Elastic search? I guess you're familiar with Auth0. Best, Michael

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________________________________ From: K-adi ***@***.***> Sent: Sunday, January 26, 2025 9:57 PM To: nrnb/GoogleSummerOfCode ***@***.***> Cc: Blinov,Michael ***@***.***>; Mention ***@***.***> Subject: Re: [nrnb/GoogleSummerOfCode] Website for VCellDB.org (Issue #249) *** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. *** Hi @vcellmike<https://urldefense.com/v3/__https://github.com/vcellmike__;!!Cn_UX_p3!l0y9G2qi3nVX90F9c19MmjjNA-chahcwupbYYlsrhkDOBbPK8VmsD2GE5DXcISn9JUh6n3WFaqY813gv4L8b5RCh$> , i'm Adil kadival, really excite to work on this project — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/nrnb/GoogleSummerOfCode/issues/249*issuecomment-2614762577__;Iw!!Cn_UX_p3!l0y9G2qi3nVX90F9c19MmjjNA-chahcwupbYYlsrhkDOBbPK8VmsD2GE5DXcISn9JUh6n3WFaqY813gv4FHHpyeg$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AG52WOAFFLVKPVBZ4TAJPVT2MWOCDAVCNFSM6AAAAABVYFUS76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMJUG43DENJXG4__;!!Cn_UX_p3!l0y9G2qi3nVX90F9c19MmjjNA-chahcwupbYYlsrhkDOBbPK8VmsD2GE5DXcISn9JUh6n3WFaqY813gv4FiPfR1P$>. You are receiving this because you were mentioned.

[adilkadivala]

Hi @vcellmike ,

Thanks for reaching out! I appreciate you taking the time to explore my projects. I hope my email will find out you,

[adilkadivala]

Hi Michael Blinov, Thanks for reaching out! I appreciate you taking the time to explore my projects. My first project admin-dashboard is a just frontend project, it has no any functionality, while finance and ai_project both are full-stack project working with propper api and database, You are right about the clerk error, so i updated my readme files, even you get any trouble, I'm providing you here all of them env for finance NEXT_PUBLIC_APP_URL=https://follow-finance.vercel.app NEXT_PUBLIC_CLERK_PUBLISHABLE_KEY=pk_test_ZXZvbHZpbmctYW50ZWxvcGUtMjIuY2xlcmsuYWNjb3VudHMuZGV2JA CLERK_PUBLISHABLE_KEY=pk_test_ZXZvbHZpbmctYW50ZWxvcGUtMjIuY2xlcmsuYWNjb3VudHMuZGV2JA CLERK_SECRET_KEY=sk_test_oEF111C9A4lzz0RRpurOZttWc2TFR3ngBMy7lWFKHA NEXT_PUBLIC_CLERK_SIGN_IN_URL=/sign-in NEXT_PUBLIC_CLERK_SIGN_UP_URL=/sign-up ***@***.*** /neondb?sslmode=require so for finance you need a csv file, so let me attach it too. env for ai_project NEXT_PUBLIC_CLERK_PUBLISHABLE_KEY=pk_test_aW50aW1hdGUtc2NvcnBpb24tNTkuY2xlcmsuYWNjb3VudHMuZGV2JA CLERK_SECRET_KEY=sk_test_ghH2xd6q45vdfUz8qxlTimumPkt1Xm0QeO9hrpwtzy NEXT_PUBLIC_CLERK_SIGN_IN_URL=/sign-in NEXT_PUBLIC_CLERK_SIGN_UP_URL=/sign-up NEXT_PUBLIC_GOOGLE_GEMINI_API_KEY=AIzaSyBOBHhEJuHwS9wojjhTuO-WnvioZrwhie4 ***@***.*** /neondb?sslmode=require SUBSCRIPTION_PLAN__ID=plan_ObWZzrrLov7CnN RAZORPAY_PAYMENT_KEY_ID=rzp_test_8peqTc6aSSqwJX RAZORPAY_PAYMENT_KEY_SECRET=pgP5iz6TQb9EnJIbWUaTqMMr NEXT_PUBLIC_RAZORPAY_PAYMENT_KEY_ID=rzp_test_8peqTc6aSSqwJX even if you have not time then I have also attached a hosted urls on particular repo. of projects... Thanks for reachout me, eagerly waiting for your reply.. best regards, Message ID: ***@***.***>

…

[adilkadivala]

if any reason google gemini api not works, please use this one NEXT_PUBLIC_GOOGLE_GEMINI_API_KEY = AIzaSyD12_J9FuoX0hyPX4Ou8ef3KBXoWSPezdE

…

On Wed, Jan 29, 2025 at 7:53 PM Adil Kadival ***@***.***> wrote: Hi Michael Blinov, Thanks for reaching out! I appreciate you taking the time to explore my projects. My first project admin-dashboard is a just frontend project, it has no any functionality, while finance and ai_project both are full-stack project working with propper api and database, You are right about the clerk error, so i updated my readme files, even you get any trouble, I'm providing you here all of them env for finance NEXT_PUBLIC_APP_URL=https://follow-finance.vercel.app NEXT_PUBLIC_CLERK_PUBLISHABLE_KEY=pk_test_ZXZvbHZpbmctYW50ZWxvcGUtMjIuY2xlcmsuYWNjb3VudHMuZGV2JA CLERK_PUBLISHABLE_KEY=pk_test_ZXZvbHZpbmctYW50ZWxvcGUtMjIuY2xlcmsuYWNjb3VudHMuZGV2JA CLERK_SECRET_KEY=sk_test_oEF111C9A4lzz0RRpurOZttWc2TFR3ngBMy7lWFKHA NEXT_PUBLIC_CLERK_SIGN_IN_URL=/sign-in NEXT_PUBLIC_CLERK_SIGN_UP_URL=/sign-up ***@***.*** /neondb?sslmode=require so for finance you need a csv file, so let me attach it too. env for ai_project NEXT_PUBLIC_CLERK_PUBLISHABLE_KEY=pk_test_aW50aW1hdGUtc2NvcnBpb24tNTkuY2xlcmsuYWNjb3VudHMuZGV2JA CLERK_SECRET_KEY=sk_test_ghH2xd6q45vdfUz8qxlTimumPkt1Xm0QeO9hrpwtzy NEXT_PUBLIC_CLERK_SIGN_IN_URL=/sign-in NEXT_PUBLIC_CLERK_SIGN_UP_URL=/sign-up NEXT_PUBLIC_GOOGLE_GEMINI_API_KEY=AIzaSyBOBHhEJuHwS9wojjhTuO-WnvioZrwhie4 ***@***.*** /neondb?sslmode=require SUBSCRIPTION_PLAN__ID=plan_ObWZzrrLov7CnN RAZORPAY_PAYMENT_KEY_ID=rzp_test_8peqTc6aSSqwJX RAZORPAY_PAYMENT_KEY_SECRET=pgP5iz6TQb9EnJIbWUaTqMMr NEXT_PUBLIC_RAZORPAY_PAYMENT_KEY_ID=rzp_test_8peqTc6aSSqwJX even if you have not time then I have also attached a hosted urls on particular repo. of projects... Thanks for reachout me, eagerly waiting for your reply.. best regards, Message ID: ***@***.***> >

[adilkadivala]

yeh I'm familiar with Elastic search, and with Auth0, too.

[shafayat666]

Hi, I'm a fellow learner from Bangladesh. Is there any sort of community where I can talk about this project? @vcellmike

[shafayat666]

I tried to clone the repo in my local system, but it gives me the following error:

error: invalid path 'files/CM_PM12648679_MB10::Substrate_depletion_oscillator.vcml'

I am using Windows 11 and I think the issue is with the path convention. :: is invalid for NTFS system if I'm not wrong.
Couldn't find the issue tracker so I am saying it here.

[vcellmike]

Hello all,

The deployed version uses the wrong API call to VCell database. To run the local copy of the vcelldb, you need to change the API call everywhere to https://vcell.cam.uchc.edu/api/v0/biomodel. After that, you should be able to do a search (which is now not good - needs to be fixed, but you get some results) and see multiple pages per model).

[shafayat666]

Thank you for the update. @vcellmike

[shafayat666]

Hi @vcellmike . Updated the API as per you provided and created a PR. Hoping to get your feedback on it. I am working to improve the search. Hoping for success.