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software:topical:lifescience

Software for LifeScience Data Analyis

This page is currently under construction. It will hardly ever display a comprehensive/complete list:

  • We install many new tools upon request and it is hard to keep track documenting them all.
  • Software compiled / installed locally by projects is not supported by the HPC team and cannot be displayed here.

Links which are displayed in red, do not exist, yet. Any contribution or suggestion is welcome.

A note on limitations:

  • Benchmarks displayed on these pages are only benchmarks with respect to speed. The values are valid only for the given parameters and may greatly vary for deviating parameters or input. (You may indicate deviating experiences to us.)
  • We strive to improve the beauty and information content of this page. However, the conducted science is up to you as a user - whether or not a particular program invocation (the arguments supplied) actually make sense for your scientific question is up to you to decide.

News

News on software in bioinformatics and related stuff is distributed via a mailing list (low traffic). You can subscribe, too. You may also distribute and share information using this list.

Contributing

Yes, please! Please get in touch with us, if you want to benchmark or contribute wrapper scripts. We created some repositories and would be delighted to you to the list of contributors. Also, contributions to this wiki (reports, suggestions, error notes) are welcome!

Installed Life Science Software

Life science software is installed on Mogon I and II in the bio module category1).

To list the available tools, you can type:

module av bio/ |& cut -f2 -d '/' | uniq

A subsequent

module av|& grep <tool of interest>

, where tool of interest is copy-pasted from the output above, will show the respective versions for that software.

You can ask for updates on a particular software or to install previously not supported software via our webpage.

If an installed tool is not listed on this page, respectively its underlying links, you may contribute this (its a wiki!) or ask for further documentation.

NGS & Co.

NGS Preprocessing Software and other Quality Checks

Mapping Tools

Intermediate Processing

Annotation Tools / Local Search Tools

Various -- Software Collections

  • SeqAn – efficient applications of different areas *
  • BBMap – short read aligner + other tools *

Genome Assembly

Evolutionary & Phylogenetics Software Tools

Molecular Docking Tools

Molecular Dynamics Simulations

Molecular Dynamics (MD) simulations are not confined to condensed matter physics, but of interest in the life sciences as well. They are, however, thematically attributed to physics. This page, therefore, merely indicates a link:

Development

What Else?

This wiki does not cover your topic / favorite software? Please let us know.

  1. We can install your software, which frequently is better than to install software yourself2), because:
    • we install software in an optimized fashion
    • if installed as a module, we made the commitment to support the software, if there are issues with the module, the batch system or I/O3)
  2. Writing wrapper scripts for otherwise non-performant applications can take time. We still encourage to approach us and ask us, before being stuck in a project.

Any contribution (a script, an idea, a reported issue, feature request, documentation, test data, own benchmark, etc.) is welcome! Particularly, section links labeled with “*” require attention4).

Tired of Software as a Service?

  • You have the option to collaborate on specific setups or if a specific tool needs to be written.
  • Any feedback will help.
1)
This is true with a few exceptions, e.g. AutoDock.
2)
With the exception of abandonware, crappy software, scripts which can be installed with pip, cran, etc..
3)
but, of course, not with respect to bugs within the software
4)
Missing links wait to be filled with content - a re-structuring might also occur.
software/topical/lifescience.txt · Last modified: 2019/07/30 12:33 by meesters