[Debichem-devel] Looking for a mentor -- multiscale molecular modeling package MMB (and molmodel)

[Samuel Flores]

Hej Andreas,

Sure, sounds great!  Thanks very much for offering to help. Sorry I have been so slow -- I have lots of administrative and pedagogical responsibility, and no students that might compile c++. 

I thought I saw OpenMM is already packaged. If not it should have an MIT license so might not even require permission from Simbios to package up. Molmodel is likewise also on MIT license, and I believe as maintainer I should have the authority to give permission to package that anyway. In any case Michael Sherman (former software architect at Simbios) or Joy Ku (current dissemination director) could clarify any permissions issue.

With kind regards,

Sam

> On 4 Mar 2019, at 13:15, Andreas Tille <tille at debian.org> wrote:
> 
> Hi,
> 
> On Wed, Feb 27, 2019 at 10:02:32AM +0200, Andrius Merkys wrote:
>> Hi Samuel,
>> 
>> On 2019-02-26 18:27, Samuel Flores wrote:
>>> I would like some help packaging MacroMoleculeBuilder (MMB) for distribution in Debian or Ubuntu. It is a mature piece of code, used to publish many scientific articles in structural bioinformatics and structural and molecular biology. It has been downloaded thousands of times.
>> 
>> I would gladly help with the packaging of this modeling tool.
>> 
>>> I would be happy to change MMB's license to be compatible with this process.
>> 
>> You are absolutely right to start with the license check. Debian accepts
>> only those licenses that are compatible with Debian Free Software Guides
>> [1]. You can find (incomplete) list of DFSG-compatible licenses here [2].
>> 
>> [1] http://www.debian.org/social_contract#guidelines
>> [2] https://wiki.debian.org/DFSGLicenses
>> 
>>> MMB requires OpenMM, simbody, and SeqAn, I believe all of these are already packaged. It also requires SimTK molmodel which is not packaged -- I am the maintainer of molmodel and would like to package this as well. Molmodel is not hard to compile, but it does use cmake. 
>> 
>> OpenMM and molmodel are not yet in Debian, AFAIK. Thus they have to be
>> packaged before the MMB. To start with, I would suggest reading the
>> introduction to packaging [3], as Andrey has advised.
> 
> I'd recommend to discuss this with DebiChem team (list in CC)
> 
>> Andrius Merkys
>> Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
>> LT-10257 Vilnius, Lithuania
> 
> See you soon at Debian Med sprint
> 
>      Andreas. 
> 
> -- 
> http://fam-tille.de



Samuel Coulbourn Flores, Docent
Dean of the Swedish National Graduate School in Medical Bioinformatics
Studierektor för den nationella forskarskolan inom medicinsk bioinformatik

Department of Biochemistry and Biophysics
Stockholm University

Visiting:
SciLifeLab A6220 (Alpha Tr. 6)

Deliveries:
Samuel Flores
Stockholms Universitet, Org # 202100-3062
Tomtebodavägen 23a
171 65 Solna
SWEDEN

Mobil: +46.706000464
Mexank: 0816-3949
skype: samuelfloresc
QQ: 3236579471

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