Hi Andreu, I am definitely making my source code available to everyone, under open source agreement. I am not going the commercial route. And while I will protect my intellectual property, I am not going the patent route. I am not a believer of the whole aggressive "stop people doing stuff" idea.
I should have said that I am making this open source, at the start. The main reason I am delaying in making it open source, is that I don't have a C++ version yet, so I have nothing to offer. And also I find source forge awkward to use and wastes a lot of time, compared to me just uploading the source code directly to my website and just putting an agreement saying "this is open source". As for writing a paper... I don't really have the background in University to write a paper, meaning it would take me a lot longer to do than someone experienced in writing papers. And to be honest I feel it would distract me from my main goal, which is to spend my time doing something productive. I would rather someone else write a paper for me :) I think this would be a fair arrangement. But I am happy to explain my algorithm. I think I should write up a document however explaining it. Maybe not in academia, more in software developer style. Thanks for all the interest and suggestion everyone. It's helping a lot. On 12 Feb 2008, at 15:45, Andreu Alibés wrote: > Why not making the code available to everybody in an Open Source > repository like sourceforge? > > A > > On Feb 11, 2008 5:21 PM, Theodore H. Smith <[EMAIL PROTECTED]> wrote: >> >> Hi everyone, >> >> So I've been working, on and off, on this algorithm for quite a while >> now. It's basically an invention of mine. It is a "blast-like" >> algorithm, in that it does "Fuzzy lookup" operations across a >> database >> of letters. I am designing this algorithm to be useful for bio- >> informatics, this is the main field I am initially targetting. >> >> The database will be filled with protein sequences, and the search >> across the database will be another protein sequence. The algorithm >> has a "scoring matrix", which can accept different protein >> replacement >> scores. The cost of inserting letters (protein letters) can be >> configured also. >> >> In this sense, it's no different to Smith-Waterman. The same input, >> the same output! >> >> The real difference from Smith-Waterman, is it's speed. My algorithm >> will be hugely faster. This is because I use many techniques to avoid >> processing unnecessary parts of the Smith-Waterman matrix. >> >> I also use many tricks to reuse computations across various proteins. >> For example, the matrix for protein "ABCDE", is identical, at first >> anyhow, for the matrix for "ABCDEFG". This means if I have both >> proteins "ABCDE", and "ABCDEFG" in my protein database, I can test >> both of them against the search query, in almost half the time. My >> algorithm also runs in logarithmic-time with respect to the size of >> the database. Basically, bigger databases run disproportionately >> faster. >> >> I want to turn this algorithm, into something useful for people. My >> first challenge here, is to answer the question "is this algorithm >> faster, or better than BLAST". If it is not faster, my algorithm >> basically has little use. But I have good hopes it will be faster! I >> am very good with these sort of things, you see :) Speed is my >> strong- >> point. >> >> Currently, I do not know about the speed, because I haven't >> implemented a C++ version of my algorithm, or a good speed testing >> framework. >> >> I do however know that my algorithm is more accurate than BLAST, >> because it is just as accurate as SSEARCH, as mine uses the Smith- >> Waterman algorithm. Whereas BLAST uses a heuristic, intelligent >> guess- >> work basically. A fine heuristic, but still a heuristic. Mine is >> methodological, not heuristic based. >> >> So here is what I am looking for! >> >> I am hoping, that someone in the field will be able to offer me >> guidance, interest, enthusiasm, suggestions and maybe even do some >> testing for me. >> >> Perhaps a student doing a bio-informatics related degree, who would >> like to write a paper on an alternative way of processing protein >> databases. My invention could be an interesting subject for a paper. >> >> Or perhaps a researcher who just has an interest in these sort of >> things! Perhaps a researcher who feels there must be a better way of >> doing these things. Or anyone really in this field with the time and >> interest, and feels helping me could help him (or her) too in some >> way. >> >> I'd like someone I can ask a lot of questions to, and show my >> software >> to, and explain my hopes what I can achieve with it. >> >> Basically, my first question to you, would be "how would I set this >> up >> to be useful for someone", and "how would I test it's usefulness, >> what >> would you need to know about my algorithm that you would decide to >> use >> it over blast" >> >> It's sort of a vague question from me, like "what do you need me to >> do", but... well that's where I am right now. Sort of a bit on the >> outside hoping someone on the inside will show me something. >> >> So it's an opportunity to tell me what you want, basically!! Tell me, >> and I might just make it. >> >> Who knows? Maybe one day in a few years time, everyone will be using >> this "ElfDataFuzzy" algorithm that I invented, instead of BLAST! You >> might be part of something. >> >> Thanks to anyone who replies! >> >> -- >> http://elfdata.com/plugin/ >> "String processing, done right" >> >> >> >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > Andreu Alibés, PhD > Systems Biology Program - Center for Genomic Regulation > c/ Dr. Aiguader 88, 08003 Barcelona, Spain > Phone: +34 93 316 0258 > http://aalibes.googlepages.com/ > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb -- http://elfdata.com/plugin/ "String processing, done right" _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
