csbiology / deepstabp

A small web ui and python api service to predict protein melting point temperatures.

DeepStabP - WebUI

Install pre-requisites

You'll need to install the following pre-requisites in order to build SAFE applications

You can check if you have these installed with the cmd command written below each 👀

• The .NET 6 SDK
  • test with dotnet --list-sdks
• node.js (v16.x || v18.x)
  • Will most of the time also install npm
  • test with node --version
• npm (>v8.x)
  • test with npm --version
• Python 3.9 (used for ml api)
  • test with py --version

Starting the application

1. Before you run the project for the first time only you must install dotnet "local tools" with this command:

dotnet tool restore

2. To concurrently run the server, client and the python fastapi components in watch mode use the following command:

./build.cmd

Then open http://localhost:8080 in your browser for the web ui and http://localhost:8000/docs for the python api OpenApi docs.

Docker

Environment

• DEEPSTABP_URL: Sets the url for the api predictor backend.

  Default: "http://localhost:8000"

Publish

1. Before publishing make sure to commit all changes and update the version with

   ./build.cmd releasenotes semver:xxx, where xxx is the required version [major|minor|patch].

2. If the backend api was changed update the static version string in src/api/app/main.py predictor_version.

3. Use ./build.cmd dockerbundle [--uionly] to create new docker images

4. Use ./build.cmd dockertest [--uionly] to run both images for testing.

   This might take some time as the api image will downloag ~7GB model. Use the --uionly option to only bundle/test the ui and not the api.

5. Use ./build.cmd dockerpublish, after logging into the csbdocker account (docker login) to push both images to dockerhub

6. Use ./build.cmd dockertestproduction to pull and test both images from remote as docker compose stack.

   Ui will be accessible on localhost:5000 and api on localhost:8000

Supported formats

deepSTAPp expects input in either the FASTA format or as pure amino acid sequence. The FASTA format consists of two building blocks. The first is a description which explains the following sequence. This description starts with ">" and is written in a single line. The amino acid sequence follows in the next line and can span multiple lines. An example for this format is:

>sp|A0A178WF56|CSTM3_ARATH Protein CYSTEINE-RICH TRANSMEMBRANE MODULE 3 OS=Arabidopsis thaliana OX=3702 GN=CYSTM3 PE=1 SV=1
MAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAA
MCCCCVLDCVF
>sp|A1YKT1|TCP18_ARATH Transcription factor TCP18 OS=Arabidopsis thaliana OX=3702 GN=TCP18 PE=1 SV=1
MNNNIFSTTTTINDDYMLFPYNDHYSSQPLLPFSPSSSINDILIHSTSNTSNNHLDHHHQ
FQQPSPFSHFEFAPDCALLTSFHPENNGHDDNQTIPNDNHHPSLHFPLNNTIVEQPTEPS
ETINLIEDSQRISTSQDPKMKKAKKPSRTDRHSKIKTAKGTRDRRMRLSLDVAKELFGLQ
DMLGFDKASKTVEWLLTQAKPEIIKIATTLSHHGCFSSGDESHIRPVLGSMDTSSDLCEL
ASMWTVDDRGSNTNTTETRGNKVDGRSMRGKRKRPEPRTPILKKLSKEERAKARERAKGR
TMEKMMMKMKGRSQLVKVVEEDAHDHGEIIKNNNRSQVNRSSFEMTHCEDKIEELCKNDR
FAVCNEFIMNKKDHISNESYDLVNYKPNSSFPVINHHRSQGAANSIEQHQFTDLHYSFGA
KPRDLMHNYQNMY

deepSTABp was developed with the assumption that the description follows the standard used by the Universal Protein Resource (Uniprot) and only returns the Uniprot ID as description in the output table. This can be circumvented by removing the "|" in the description. In this case the complete description gets returned.

The only other supported format are pure amino acid sequences. An example for this format is:

MAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAA
MCCCCVLDCVF

This format can only be used for a single amino acid sequence. Multiple amino acid sequences must be in the following format:

>!MAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAA
MCCCCVLDCVF
>!MNNNIFSTTTTINDDYMLFPYNDHYSSQPLLPFSPSSSINDILIHSTSNTSNNHLDHHHQ
FQQPSPFSHFEFAPDCALLTSFHPENNGHDDNQTIPNDNHHPSLHFPLNNTIVEQPTEPS
ETINLIEDSQRISTSQDPKMKKAKKPSRTDRHSKIKTAKGTRDRRMRLSLDVAKELFGLQ
DMLGFDKASKTVEWLLTQAKPEIIKIATTLSHHGCFSSGDESHIRPVLGSMDTSSDLCEL
ASMWTVDDRGSNTNTTETRGNKVDGRSMRGKRKRPEPRTPILKKLSKEERAKARERAKGR
TMEKMMMKMKGRSQLVKVVEEDAHDHGEIIKNNNRSQVNRSSFEMTHCEDKIEELCKNDR
FAVCNEFIMNKKDHISNESYDLVNYKPNSSFPVINHHRSQGAANSIEQHQFTDLHYSFGA
KPRDLMHNYQNMY

deepstabp's Issues

Change output table headers

The current output table has "mt" as header. Either change it towards "melting temperature" or towards "Tm". The current "mt" makes it look like it was a typo and not a abbreviation for melting temperature. Also add a metric to the same header to show that we use degree Celsius.
I would suggest one of these two to fix both problems:
Tm [°C]
Melting temperature [°C]

Stop running job when clicking on closing result modal in any way

Web application not operating

Hello,
i got a reply that the web application is again running but this does not seem to be the case. It was able to launch it end of last week but today I just get a message that https://csb-deepstabp.bio.rptu.de/ is not available. Could it be a problem of my local computer/network? But it is then strange that i could run the application without problems last week.
Would be great if you could give me some feedback.
Thanks and best regards!

Web application not working

I tried to use https://csb-deepstabp.bio.rptu.de/ with google chrome (04/10/2023) but got the following error message:
Die Website ist nicht erreichbar
Prüfe, ob „csb-deepstabp.bio.rptu.de“ einen Tippfehler enthält.
Wenn die URL keinen Tippfehler enthält, kannst du die Windows-Netzwerkdiagnose durchführen.
DNS_PROBE_FINISHED_NXDOMAIN
Is the page currently not maintained?

Increase searchability with google

Sources:

https://ahrefs.com/blog/seo-meta-tags/
https://www.webfx.com/seo/learn/structured-data/
https://www.google.com/webmasters/markup-helper/u/0/
https://developers.google.com/search/docs/appearance/structured-data/search-gallery

localization

Good work, but the tools are too hard to use locally

Add contact options

• Add contact subpage or add info to footer.
• Replace email placeholder in "Privacy Policy" subpage.

Add example options

Add one click example options.

Maybe something similiar to open api docs.

Dropdown? Several buttons?

"Large" fasta files

The website can not handle fasta files that are larger than~ 20Kb. The website returns task was cancelled if I try to use a bigger fasta file. The timeout either needs to be increased or we need to find a different solution to the problem to avoid this.
This is a real problem as we say in the paper that it is possible to do whole proteome analysis with deepSTABp which would mean it must be possible to run the tool with fasta files with sizes of 80'000 to 100'000 Kb.

Index website using google search console

https://search.google.com/u/1/search-console/welcome?action=inspect&utm_medium=referral&utm_campaign=9012289

Web application not working

The deepstabp web application at https://csb-deepstabp.bio.rptu.de/ was now running at the end of last week but when I tried today i again got an error message that it is not available.