Caprion data analysis

Welcome!

This repository/site is dedicated to protein/peptide quantitative trait analysis using the Caprion platform, which is organised chonologically/logistically into the following sections.

Pilot studies

• autoencoder
• gwas2
• Pilot studies

Analysis

• Protein analysis
• Peptide analysis
• Miscellaneous analysis

Additional information

• Caprion panel
• Notes

Local file/web browsing

A web-style navigation is furnised via a port number, e.g., 8000,

cd /rds/project/rds-zuZwCZMsS0w/Caprion_proteomics/analysis

module load ceuadmin/edge

export pn=8000
if lsof -i :${pn}; then
    echo "Port ${pn} is already in use' try another one."
else
    python3 -m http.server ${pn} &
    server_pid=$!
    edge http://localhost:${pn} &
fi

where the port number can be released with kill $server_pid (can be checked with ps). In case it does now show, use

edge --user-data-dir=${TMPDIR} http://localhost:${pn} &

in replace of ~/.config/microsoft-edge, where TMPDIR is a directory name.

One could browse files as well as mirrors of two web sites.

1. SRCF. The mirror is within the following subdirectory: /srcf.
2. Web site. This is from /site as above.
3. Isotopes associated with >1 proteins, /dup/json/dup.htm

Non-CSD3 browser(s)

This approach seems less problematic with user-data-dir mentioned above. We can again set up tunneling from CSD3 with

python3 -m http.server 8000 &
hostname

Once succeeded, we establish the connection elsewhere.

ssh -4 -L 8080:127.0.0.1:8000 -fN jhz22@${hostname}.hpc.cam.ac.uk

where hostname from CSD3 and ${hostname} have to be the same. We can then browse http://127.0.0.1:8080.