Thank Linas. I will try my best to achieve something with very little supervision.
With best regards, Abu On Sat, 2 Mar 2019 at 00:31, Linas Vepstas <[email protected]> wrote: > 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 > <https://groups.google.com/d/msgid/opencog/CAHrUA362%3DM96ta7p%3DjPnLvR8GG%2BzUe%2BkZpBKXZCi-QbnQgTRZA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "opencog" group. 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