Abu, And just to be clear -- when Ben says "a brave soul", what he means is that it is very much a roll-up-your-sleeves-and-do-it-yourself project. There are no easy-to-use push-button GUI's for this: you would have to read about and understand a lot of non-bioinformatics systems, and then figure out, with very little supervision or guidance, how to hook them together.
(Totally off-topic -- there was an effort to have Jupyter notebooks for opencog -- what ever happened to that? The point was that a Jupyter notebook would be a way of show-casing some kind of data-flow that people could actually use ... anyone know anything about this?) --linas On Fri, Mar 1, 2019 at 5:59 PM Ben Goertzel <[email protected]> wrote: > The MOSES-for-supervised-learning stuff is a bit specialized, and > doesn't use the main OpenCog codebase, MOSES is a standalone system > > However Nil wrote code for importing learned MOSES models into the > Atomspace, and once you've done that you can play with PLN inference > or other tools for combining MOSES models w/ other knowledge > > A great project for a brave soul right now would be > > -- run MOSES on some categorial SNP or gene expression data to get a > big diverse model ensemble > > -- load these models into Atomspace > > -- use Nil's new Pattern Miner to find surprising patterns among the > MOSES models > > Then one could bring PLN into the story to integrate, say, Gene > Ontology into the surprisingness assessment... > > ben > > On Sat, Mar 2, 2019 at 7:41 AM Abu Naser <[email protected]> wrote: > > > > Hi Ben, > > > > Thank your for responding my queries. I will try to find the papers and > guessing you are one of the authors of the papers. It would be very useful > for me if I could get Bioinfromatics related toy examples to play around, > which will help me to get to know the opencog code. Hope Mike will point me > to one of those example code. > > > > With kind regards, > > > > Abu > > > > On Fri, 1 Mar 2019 at 23:14, Ben Goertzel <[email protected]> wrote: > >> > >> There are two pieces to what we've been doing w/ OpenCog for > bioinformatics > >> > >> 1) supervised classification of genomics datasets (e.g. SNPs, gene > >> expression) using MOSES > >> > >> 2) integration of various ontologies into the Atomspace, import of > >> MOSES classification models into the Atomspace, and use of PLN > >> reasoning (currently on a pretty ad hoc, human guided basis) to do > >> inference based on this combined data > >> > >> There are publications on both of these things, though I don't have > >> time to dig up the URL right now, and Mike can point you to the > >> code... > >> > >> ben > >> > >> On Sat, Mar 2, 2019 at 5:51 AM Linas Vepstas <[email protected]> > wrote: > >> > > >> > Hi, > >> > > >> > Opencog has many parts to it.There is an agi-bio part for > bioinformatics but it seems slim, and I think the main part of that system > is somewhere else. I'm hoping Mike Duncan can respond in more detail. > >> > > >> > --linas > >> > > >> > On Fri, Mar 1, 2019 at 1:15 PM Abu Naser <[email protected]> wrote: > >> >> > >> >> Hello Everyone, > >> >> > >> >> I have just installed opencog on Ubuntu. I am a biologist and wish > to use opencog for solving biological problems. I have been wondering > whether there is any tutorial related to Bioinformatics. Please let me know. > >> >> > >> >> With best regards, > >> >> > >> >> Abu > >> >> > >> >> -- > >> >> You received this message because you are subscribed to the Google > Groups "opencog" group. > >> >> To unsubscribe from this group and stop receiving emails from it, > send an email to [email protected]. > >> >> To post to this group, send email to [email protected]. > >> >> Visit this group at https://groups.google.com/group/opencog. > >> >> To view this discussion on the web visit > https://groups.google.com/d/msgid/opencog/b91a8dda-25db-48ea-80ed-776fed30dea6%40googlegroups.com > . > >> >> For more options, visit https://groups.google.com/d/optout. > >> > > >> > > >> > > >> > -- > >> > cassette tapes - analog TV - film cameras - you > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > Groups "opencog" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send an email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at https://groups.google.com/group/opencog. > >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/opencog/CAHrUA34wuXH1z%3DiDwE9_HX7%2BN04SPyTHjzSp8hKPR6%2Bgih1rXA%40mail.gmail.com > . > >> > For more options, visit https://groups.google.com/d/optout. > >> > >> > >> > >> -- > >> Ben Goertzel, PhD > >> http://goertzel.org > >> > >> "Listen: This world is the lunatic's sphere, / Don't always agree > >> it's real. / Even with my feet upon it / And the postman knowing my > >> door / My address is somewhere else." -- Hafiz > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups "opencog" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an email to [email protected]. > >> To post to this group, send email to [email protected]. > >> Visit this group at https://groups.google.com/group/opencog. > >> To view this discussion on the web visit > https://groups.google.com/d/msgid/opencog/CACYTDBe4hX_MK2x2wXRmZ6ZiVqGO5Q48FC%3DJoyPYWAUYOv3VBQ%40mail.gmail.com > . > >> For more options, visit https://groups.google.com/d/optout. > > > > -- > > You received this message because you are subscribed to the Google > Groups "opencog" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at https://groups.google.com/group/opencog. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/opencog/CAMw3wdhhdkdNMGLGPxf0aRZOG9VkaU05sNdc87%2B7TOYYiZi0tg%40mail.gmail.com > . > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Ben Goertzel, PhD > http://goertzel.org > > "Listen: This world is the lunatic's sphere, / Don't always agree > it's real. / Even with my feet upon it / And the postman knowing my > door / My address is somewhere else." -- Hafiz > > -- > You received this message because you are subscribed to the Google Groups > "opencog" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/opencog. > To view this discussion on the web visit > https://groups.google.com/d/msgid/opencog/CACYTDBf4tv8-sJ9FV%3DFbGwb9ny3GbZ%3DYRZWSS%2BbpKCjOYnBKpw%40mail.gmail.com > . > For more options, visit https://groups.google.com/d/optout. > -- cassette tapes - analog TV - film cameras - you -- You received this message because you are subscribed to the Google Groups "opencog" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/opencog. To view this discussion on the web visit https://groups.google.com/d/msgid/opencog/CAHrUA362%3DM96ta7p%3DjPnLvR8GG%2BzUe%2BkZpBKXZCi-QbnQgTRZA%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
