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https://github.com/csbiology/deepstabp
A small web ui and python api service to predict protein melting point temperatures.
https://github.com/csbiology/deepstabp
Last synced: 30 days ago
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A small web ui and python api service to predict protein melting point temperatures.
- Host: GitHub
- URL: https://github.com/csbiology/deepstabp
- Owner: CSBiology
- License: mit
- Created: 2023-01-09T13:46:55.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-02-01T14:27:30.000Z (11 months ago)
- Last Synced: 2024-03-19T06:01:16.557Z (10 months ago)
- Language: F#
- Homepage: https://csb-deepstabp.bio.rptu.de
- Size: 140 MB
- Stars: 11
- Watchers: 3
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](https://dotnet.microsoft.com/en-us/download/dotnet/6.0)
- test with `dotnet --list-sdks`
- [node.js (v16.x || v18.x)](https://nodejs.org/en)
- Will most of the time also install npm
- test with `node --version`
- [npm (>v8.x)](https://docs.npmjs.com/downloading-and-installing-node-js-and-npm)
- test with `npm --version`
- [Python 3.9](https://www.python.org/downloads/release/python-3916/) (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:
```bash
dotnet tool restore
```
2. To concurrently run the server, client and the python fastapi components in watch mode use the following command:
```bash
./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](https://www.uniprot.org/)) 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
```