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