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    Stian Soiland-Reyes
    @stain
    exactly.. often just a particular choice of technology (say RDF, Java, XML, Docker, Web Services) is presumed to automatically fulfill various unexpressed non-functional requirements - but if nobody tells the engineers it won't be so because they need to make shortcuts to get it to work in time :)
    I guess we could add HPC to the list.. "Look, it's got lots of processors.. why isn't it faster?"
    Stian Soiland-Reyes
    @stain
    Stian Soiland-Reyes
    @stain
    Stian Soiland-Reyes
    @stain
    @edinburghadam http://phenomenal-h2020.eu/home/ -- btw. I know well Ola Spjuth in the tweet there. :)
    Stian Soiland-Reyes
    @stain
    @rapostolo - where could I add my https://www.big-data-europe.eu/the-open-phacts-pilot-second-hangout-for-the-health-societal-challenge/ on the bioexcel website? Does it count as a Webinar even though it's not a BioExcel Webinar (tm)..?
    Rossen Apostolov
    @rapostolo
    will you join for the WP4 call right now?
    Stian Soiland-Reyes
    @stain
    yes
    Rossen Apostolov
    @rapostolo
    I think it's ok to put it as a blog post in the webinar category but without the "webinar#6:" etc. notation
    Stian Soiland-Reyes
    @stain
    just to chec.. can HADDOCK dock a protein and a small molecule (a drug compound from drugbank - e.g. DB00398)? It seems to only want PDB files.
    Stian Soiland-Reyes
    @stain
    but probably the positions in there don't make much sense
    Alexandre Bonvin
    @amjjbonvin
    Indeed it requires PDB format. But the link you are giving above is PDB format. BUT: the atom names should be unique and this is not the case here...
    Stian Soiland-Reyes
    @stain
    hm.. this has been a problem for a while - it's the kind of thing in Open PHACTS we flag when we put it through the ChemSpider-based Chemical Registration Service - but I think we load from SDF files which I guess is more generic that PDB. We can use a pre-processing shims in the workflow to fix it.
    Alexandre Bonvin
    @amjjbonvin
    do you have a script to fix the atom names automatically?
    Stian Soiland-Reyes
    @stain
    I think OpenBabel might be able to do it
    Stian Soiland-Reyes
    @stain
    Hi, this is the public room for BioExcel. We're in Barcelona for All Hands meeting - join our private chat at the https://gitter.im/bioexcel room - ask me here and I can grant you access if you don't already have it. (All GitHub users in the BioExcel organization should have access)
    Vera Matser
    @VeraMatser_twitter
    Hi Stian, can I get access to the private room?
    Marc Baaden
    @bam93
    Hi Stian, me too, please.
    Mirren White
    @mirrenwhite_twitter
    Me three, if possible!
    Stian Soiland-Reyes
    @stain
    I think you should have access now (Try Ctrl-Shift-R on http://bioexcel/ )
    Not sure that worked for non-GitHub users.. sorry. Let's try bioexcel/private instead.
    CaroleGoble
    @CaroleGoble
    hello
    Stian Soiland-Reyes
    @stain
    hi, you should now be able to join the bioexcel/private room (not sure if you have to refresh the browser?)
    Mark Abraham
    @mabraham
    private is 404 for me... how do I get my github ID mabraham blessed into the BioExcel organization?
    Stian Soiland-Reyes
    @stain
    you are blessed, my child.
    (private should work for you now - I think also you can accept the organization invite on https://github.com/bioexcel )
    Mark Abraham
    @mabraham
    i'm in, thanks
    Stian Soiland-Reyes
    @stain
    Michael R. Crusoe
    @mr-c
    FYI: Previous text in the chat window doesn't show up for late joiners :-)
    Michael R. Crusoe
    @mr-c
    Stian Soiland-Reyes
    @stain
    thanks - what do you mean.. the workflow image? It shows here with Chrome and Firefox, but not in Microsoft Edge -- is it because it's an SVG perhaps?
    I thouht <img> with SVG was finally allowed :)
    Michael R. Crusoe
    @mr-c
    ah, my privacy badger was blocking view.commonwl.org -- does it set a cookie?
    Stian Soiland-Reyes
    @stain
    ah! Sneaky.. or it could be that it's a http page embedding https?
    Michael R. Crusoe
    @mr-c
    It does set a cookie, a JSESSIONID
    Stian Soiland-Reyes
    @stain
    it doesn't need any cookie, so I have asked Mark to remove it
    common-workflow-language/cwlviewer#122
    Michael R. Crusoe
    @mr-c
    Thanks
    Stian Soiland-Reyes
    @stain
    Anyone at ISMB? The BioExcel booth is #3
    marcvdijk
    @marcvdijk
    Dear BioExcel community, I have a very general but no so easy questions. Could anyone shed some light on how big the global MD community is, statistics wise? I'm thinking about the number of users of the various MD software packages both in academia and commercial settings. Any insights here would be greatly appreciated.
    Stian Soiland-Reyes
    @stain
    I must admit I don't know.. and how do you count? Per lab or per "user"? How often qualifies as "use"? Say for GROMACS, as open source, we don't have registration requirement or "ping back" mechanism; but can count mailing list subscribers for instance. Perhaps @rapostolo has some insight?
    just the traffic at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ hints of quite a few users -- and consider that one person emailing might be in a team of several that are not on the list
    however we know that industry users might be more mailing-list-shy (or even be forbidden from asking anything in public)
    marcvdijk
    @marcvdijk
    Hello Stian, thanks for the comments. Yes it's all about the metrics. We would like to know how big the community of MD users in the life-sciences is, it may be a bold figure. I tried to get a hold of download statistics for the MD packages but it seems these are often not publicly available. Citations to MD software could be another metric but that counts only "successful" use mostly in the academic arena.
    But if considering "bold figures" what might be an estimate? In the order of 1000s, 10.000s or more.
    Alexandre Bonvin
    @amjjbonvin
    My guess would be 10000 and probably quite more
    Michael R. Crusoe
    @mr-c
    Turns out one of the people behind https://www.ubicalc.eu/ is here in Vilnius, perhaps this tool may be of interest.
    Mark Abraham
    @mabraham
    test
    Mark Abraham
    @mabraham
    yeah 10k+ is fair, given the range of bio and materials science MD packages
    there is no reasonable way to get a precise number, even if you can get agreement on the definition of user