Hi, Abu The task about travelling salesman problem used in protein folding is not such a trivial task.
These two papers I have in mind that relate to computing protein folding, regardless to OpenCog: - A Travelling Salesman Approach to Protein Conformation - 44daca495f4b0a9d9affbe68c6926cc3a751.pdf <https://pdfs.semanticscholar.org/5d48/44daca495f4b0a9d9affbe68c6926cc3a751.pdf> - A traveling salesman approach for predicting protein functions <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636333/> There were some understatements to me the last time i read those, but I hope you could resolve that, as a biologist and chemistry expert. As you will see, there are some trade offs between accuracy and speed, and I have to warn you, things get very complicated if you opt to completely simulate molecular physics. I think you would need a senior programmer for implementing this part. Also, here <http://biasmv.github.io/pv/demo.html> is an eye catchy free application link if you are about to visualize proteins (a bit complicated input, but if you manage to crunch the first papers, this would be the less painful part). Regardless to protein folding, I believe openCog has built in SAT solver among its tools (But you'll have to ask someone more expert on this matter). Once you master OpenCog SAT solving, the problem of TSP can be reduced to SAT following this paper: - 2014ICRA_SAT-TSP(submitted).pdf <https://ece.uwaterloo.ca/~sl2smith/papers/2014ICRA_SAT-TSP(submitted).pdf> A bit of logic understanding is needed, but if OpenCog has an ability to solve SAT problems, I believe that previous paper is a way to translate TSP to SAT. Once you have a logic conglomerate representing TSP, OpenCog should be able to provide you result of the shortest path (meaning a conformation with lowest energy distribution among amino acids). I'm sorry not to have the entire problem already programmed in just one application / OpenCog tool. I was planning to code some of it in some future point, but my research bent me over so many sides (mostly in general knowledge representation area), I didn't get chance to come near to coding it. I know all these guidelines pose a much work, but this is all I have for now. Oh, you might be interested in these projects, if you want to check the competition that doesn't ever sleep (thankfully): - Folding@home – Fighting disease with a world wide distributed super computer. <https://foldingathome.org/> - Solve Puzzles for Science | Foldit <https://fold.it/portal/> - Rosetta@home <http://boinc.bakerlab.org/rosetta/> Finally, if you decide to grapple with a task of this scale, you might want to consult with some of OpenCog creators (in this mailing list, very friendly and openminded people, I have to attribute), is the entire OpenCog with its SAT solver an overkill, just to have the TSP part solved. But you never know, artificial intelligence is such an inspiring area, some idea may pop up that would completely boost up the protein research field. Let me know if there are any questions I may answer. Ivan V. pet, 1. ožu 2019. u 23:03 Abu Naser <[email protected]> napisao je: > Hi Linas, > > Thank for the update. I will be waiting for Mike's response. > > With regards, > > Abu > > On Fri, 1 Mar 2019 at 21:51, 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. 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