compgenlabub/ppaxe-app repository overview

⁠What is PPaxe-app?

PPaxe is an easy to use Python app that scans MEDLINE records from PUBMED⁠ and PMC⁠ , to extract sentences describing protein-protein interactions. Upon a list of PUBMED identifiers obtained by a keyword search at NCBI-Entrez (e.g. a set of gene names or a disease), it provides with a summary of putative protein-protein interactions and the sentences of the PUBMED records that describe them. Now implements a job id to retrieve results from long searches despite disconnecting from server. You have a demo server available from https://compgen.bio.ub.edu/PPaxe⁠.

This docker container provides all the tools and libraries required by PPaxe to run the PPaxe-app web service out of the box; just follow these simple steps:

1.- get the container image:

docker pull compgenlabub/ppaxe-app

2.- start the web service container. Just remind to set the proper email settings for the environment variables, as then it can contact via email when large sets of identifiers are submitted.

docker run -d -ti --net=host \
            --env PPAXE_EUSER="your.email.user" \
            --env PPAXE_EPASSW="your.email.passwd" \
            --env PPAXE_EMAIL="[email protected]" \
            compgenlabub/ppaxe-app

The above command will start an Stanford-CoreNLP service inside the container and a Flask + Gunicorn web application to produce a simple web interface to the PPaxe libraries. You can access using a web browser on your local host by pointing the URL to http://127.0.0.1:5000/. If everything is working you should get a home page similar to the one shown in the figure below. You have some help tips available on that web form.

⁠Environment variables

Here you can find a short description of the available customizable environment vars to fit PPaxe-app to your system:

• GUNICORN_THREADS: number of threads/cores for the Gunicorn web server (defaults to 4).
• GUNICORN_TIMEOUT: gunicorn web server time out delay (defaults to 600 seconds).
• CORENLP_THREADS: set up the number of threads for the Stanford-CoreNLP annotator (defaults to 4).
• CORENLP_MAXMEM: set up the maximum amount of system memory for the Stanford-CoreNLP annotator (defaults to 4g).
• URL_BASE: if you want to define a different URL base instead of http://127.0.0.1:5000, to get proper href text urls when running behind a proxy server for instance (the corresponding links will be pointing to the right url anyway).
• PPAXE_EUSER: your email user for sending reports (defaults to "www")·
• PPAXE_EPASSW: password to connect to the email server for the previous user (defaults to "blabla").
• PPAXE_EMAIL: user's email account for sending reports (defaults to "www@localhost").

Just remember to set up the proper DNS addresses for the container; for instance, by running the following command before launching the container (or by providing those parameters to the container command-line):

export DOCKER_OPTS="--dns primary.dns.server.ip --dns secondary.dns.server.ip";

On the other hand, we provide a new parameter for debugging the execution of this app:

• PPAXE_DEBUG: running all commands in verbose mode when set to 1. Moreover, standard output and error channels are stored in a *.log and a *.err files respectively, for both Stanford-CoreNLP annotator and Gunicorn (running the PPaxe-app), into the container /ppaxe/logs folder. That folder can be accessed by mounting a volume, for instance:

docker run -d -ti --net=host \
            --env PPAXE_DEBUG=1 \
            --volume /your/path/to/ppaxe/logs:/ppaxe/logs \
            --env PPAXE_EUSER="your.email.user" \
            --env PPAXE_EPASSW="your.email.passwd" \
            --env PPAXE_EMAIL="[email protected]" \
            compgenlabub/ppaxe-app

ls -alFhrt /your/path/to/ppaxe/logs
# -rw-r--r-- 1 root   root     0 May 11 14:18 gunicorn.log
# -rw-r--r-- 1 root   root   43K May 11 14:19 core.log
# -rw-r--r-- 1 root   root   21K May 11 14:19 core.err
# -rw-r--r-- 1 root   root   906 May 11 14:19 gunicorn.err

⁠License

PPaxe project as well as the PPaxe-app are licensed under the GNU GPL3 license - see the LICENSE⁠ file for details. PPaxe uses Stanford-CoreNLP⁠ as POS-tagger (aka Parse-Of-Speech tagger), which is also under the GNU GPL3 license. This software requires Java, we have chosen openjdk provided by the Ubuntu Linux distribution (v16.04) that serves as base of the container. The web applet requires Flask⁠ and Gunicorn⁠.

⁠Publications

If you find this software tool useful for your research, we will appreciate if you cite it as follows: