I guess I'm going to throw down my own ideas and where I'm at, joining the group for a reason. I'll get back to you dalke on the puzzles.
*The Problem * My viewpoint: Cheminformatics is bringing itself into its own science. At its foundation, it serves to connect languages together amongst lots of other things. So okay the language that philosophically makes sense is SMILES because it's intended for someone like me, an organic chemist, to read it. Now if you think about it, our generation gets to have a little fun where machine representation and manipulation of chemical objects has been mostly figured out, now we just have a chemical data big bang. This is cool. And as I explore it's amazing. Now it's pretty hard to control all this data, link semantics, understand synthesis and we have a hard time talking to the general audience about what's going on. Some of it has been shut out of the limelight by statistical methods being applied on binary patterns and claiming science. New kids on the block aren't too interested in learning foundations. So what do we do? *Education * The first, is to refine education. The organic chemistry curriculum needs to change but that's a different fight. We need a designated cheminformatic curriculum to explain what cheminformatics is in the first place to a true novice. We require a basic understanding of organic chemistry and perhaps data structures. We start there. For example a first chapter could be teaching SMILES and some of the nomenclature in our field that also exists (there's a lot of material there). The algorithms that accommodate them. We also give problem sets. Easy problems help people learn. The books I have read don't give me any challenge and only tell me what happened. So maybe implement your own InChl Key algorithm. Another chapter could be how these titan databases (ZincDB, EnamineDB, pubmed) were constructed and coded in doing rapid download etc. You learn a lot doing this and I think it would be fun. So I suggest we write a proper textbook. I also think forcefields should be part of the curriculum (call me biased because I'm working on CGenFF). The impact of a good textbook is underrated. *Physical Exposure* So here's what I've done so far. I started doing conferences inviting scientists and engineers to work on problems together. The scientist presents their problem to the engineer and they work on it together. This is also part of the cheminformatic philosophy. https://www.lifescihack.com/ The one in America was more successful, In England not so much. Not as many european contacts. I was able to get funding from Mozilla Open Science Grant in 30K. I want to continue this but in a different format. I found this worked where scientists felt more heard (lots of them tend to be introverted and especially scared because of the brutality of academia, have to get angry in here...). Where I'm headed, I linked with PyData and NumFocus (more engineers, devops, UI, business, other scientists) and we are hosting a exposure/conference in Baltimore or trying to at least - have a look at the gitbook: https://mackerellgroup.gitbook.io/pydata-baltimore/ I want to expose more people and bring them to our city of Baltimore, show our NMRs off got a (900/1000) etc. What do you guys think? Any of these ideas hitting? -Sul On Thu, Dec 2, 2021 at 4:07 PM Egon Willighagen <egon.willigha...@gmail.com> wrote: > > > On Thu, Dec 2, 2021 at 6:06 AM Suliman Sharif <sharifsulim...@gmail.com> > wrote: > >> Curious to meet other folk in this group. Is there some sort of cryptic >> cheminformatic puzzle I have to solve to join? >> > > The puzzle we're all trying to solve is how we can get chemistry to become > a science where knowledge is openly shared. > > While we are seeing many promising approaches, the real solution is yet > unknown. > > Egon > > -- > ---- > BiGCaT received a NWO Open Science grant to support our research into > interoperability of biological data and knowledge: > https://www.nature.com/articles/d41586-021-03418-1 and > https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants > > ----- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> > / @egonw <https://scholar.social/@egonw> > Homepage: http://egonw.github.io/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> > ImpactStory: https://impactstory.org/u/egonwillighagen > -- *Suliman Sharif* M.Sc Medicinal Chemistry | University of California, Riverside B.Sc. Biochemistry | University of Texas at Austin sharifsulim...@gmail.com
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