I'm not sure I fully understand people's interests here & I'm not sure I'm knowledgeable enough to form my questions well. --Concerning speed: I'd expect the direction here needs to be more architectural than language specific. C on the fastest machines available next few years is not close the speed need for many problems. --Where does the modeling take place? If Bioinformatics is just a code word for sequencing & genomics, the modeling may all be done & reflecting it with good visualization may be a great step. But proteomics, cell simulation, inter-cell communication, etc. may be at a different stage & have different requirements. [I notice that BioJava is moving toward a richer model than many of us might have predicted.] Does intensive string processing suggest the right abstractions for all Bioinformatics? --What is the role of 'glue'? Is it always part of the picture, or does the need for it represent a weak architecture? --Are 'number crunching', 'glue', and 'visualization' and adequate parts list? Are repositories like Bimolecular Interaction Network Database (BIND) part of the mix? What are the implications of the FDA's move to electronic submission for clinical trials? The supply chain work might not excite the Squeak community, but I wonder about the ability of Squeak to make clinical trials understandable to lay people & suspect this may be properly part of Bioinformatics.
I'd hate to see the Squeak community limit its view of Bioinformatics to providing visualizations of the current work inspired by the genome project, valuable as that work might be. Smalltalk's strong simulation and modeling history and Squeak's particular potential for learning and education suggest a broader direction and this may be where John G. is headed.
Whether or not biologist in 2011 and 2021 will work as they do now may be worth thinking about.
-b
"Randal L. Schwartz" wrote:
"jhgillespie" == jhgillespie jhgillespie@ucdavis.edu writes:
jhgillespie> I have been playing around with bioinformatics and jhgillespie> squeak. So far I have a class heirarchy for dna, jhgillespie> protein, and coding sequences {snip} jhgillespie> {snip} I ported this stuff from my jhgillespie> lisp code, where I used calls to C routines (like jhgillespie> clustal) to do hard calculations. Perhaps something jhgillespie> similar will solve the speed problem with squeak.
{snip} it was all "perl perl perl" on the back end, "C C C" for number crunching, and "java java java" on the front end for fancy interfaces and visualization.{snip}
"Randal L. Schwartz" wrote:
"jhgillespie" == jhgillespie jhgillespie@ucdavis.edu writes:
jhgillespie> I have been playing around with bioinformatics and jhgillespie> squeak. So far I have a class heirarchy for dna, jhgillespie> protein, and coding sequences with lots of useful jhgillespie> methods, mostly things like correction formulae, codon jhgillespie> usage, base frequencies, etc. In addition, I have a jhgillespie> class that parses the Genbank flat file format and can jhgillespie> produce sequences from a menu of the documented features. jhgillespie> I have used this a bit for my own research, but am now jhgillespie> planning to teach a computational genetics course to our jhgillespie> biology undergrads using Squeak...so the pressure is on jhgillespie> to turn all this into something useful and fun. Right jhgillespie> now I can drop sequence morphs onto a playfield and jhgillespie> produce things like dot matrix plots and phylogenetic jhgillespie> trees, but visually it ain't much. The speed issue jhgillespie> hasn't been a problem because I'm not trying to do jhgillespie> anything very ambitious. I ported this stuff from my jhgillespie> lisp code, where I used calls to C routines (like jhgillespie> clustal) to do hard calculations. Perhaps something jhgillespie> similar will solve the speed problem with squeak.
I recently presented a Perl-related keynote at a gene conference in Cambridge (UK). The audience was intently listening and interested, because as I was listening to them talk, it was all "perl perl perl" on the back end, "C C C" for number crunching, and "java java java" on the front end for fancy interfaces and visualization.
I think Squeak can (and should) take over the "java" portion of this arena. But I don't think Squeak is the right mix for the Perl portions (glue) or "C" portions (crunching). All three portions have their place, so don't offend a bioinformaticist by telling them that Squeak will do it all. But clearly creating the right Morphs would let the tech-heads create better interface building blocks so that the bio-scientist non-programmers could get the job done. Especially if it ran in the browser.
Just a thought.
p.s. bioinformatics is getting BIG funding, while dotcoms are shrinking. Good people are needed. Consider a career shift. :)
-- Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095 merlyn@stonehenge.com URL:http://www.stonehenge.com/merlyn/ Perl/Unix/security consulting, Technical writing, Comedy, etc. etc. See PerlTraining.Stonehenge.com for onsite and open-enrollment Perl training!