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task #15639: Computational biology software in Maneage

Submitted by:  Mohammad Akhlaghi <makhlaghi>
Submitted on:  Wed 13 May 2020 02:39:39 PM UTC  
 
Should Start On:  Tue 12 May 2020 11:00:00 PM UTC Should be Finished on:  Tue 12 May 2020 11:00:00 PM UTC
Category:  Software Priority:  5 - Normal
Status:  Postponed Privacy:  Public
Percent Complete:  0% Assigned to:  None
Open/Closed:  Open Effort:  0.00

Wed 03 Jun 2020 12:24:50 AM UTC, comment #2: 

Yahya just recommended Glaab+2015 (https://doi.org/10.1093/bib/bbv037) which is a survey of some free software solutions in computational biology.

This can be a good resource of some free software solutions in computational biology that we can consider adding to Maneage beyond GROMACS.

So I just updated the title of this task to generally keep a registry of such software here and try building them into Maneage.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Wed 13 May 2020 04:48:39 PM UTC, comment #1: 

original submission:

> "GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles." It is a commonly used package in molecular dynamics simulations and has been proposed to be included in Maneage by Yahya Sefidbakht.
>
> Its installation instructions are also available and fortunately it seems to only depend on FFTW, other than that apparently it just needs a C compiler!
>
> So it should be fairly easy to include it in the `high-level.mk' step. Surena, do have time to try adding it to Maneage?

Surena Fatemi <surena>
Project Member
Wed 13 May 2020 02:39:39 PM UTC, original submission:  

"GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles." It is a commonly used package in molecular dynamics simulations and has been proposed to be included in Maneage by Yahya Sefidbakht.

Its installation instructions are also available and fortunately it seems to only depend on FFTW, other than that apparently it just needs a C compiler!

So it should be fairly easy to include it in the `high-level.mk' step. Surena, do have time to try adding it to Maneage?

Mohammad Akhlaghi <makhlaghi>
Project Administrator

 

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    Follow 3 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2020-06-03 makhlaghi SummaryBuilding GROMACS in Maneage => Computational biology software in Maneage
    2020-05-13 makhlaghi Carbon-Copy- => Added surenaftm@gmail.com
        Carbon-Copy- => Added y.sefidbakht@gmail.com

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