Humberto Ortiz Zuazaga wrote: > > Jeff, post it to the list, I don't see any point in keeping it a secret. Since their design is so close to ours, I am a bit concerned that NetGenics may _claim_ that we stole it. On the other hand, we've been discussing Loci in an open forum for a year now, so maybe they stole _our_ design :-) Seriously, we are dealing with a commercial entity, and they get pretty nasty when it comes to intellectual property, as I have had first hand experience with such matters. Nevertheless, I'll post it. If NetGenics complains, I'll tell them to go bite me. Gary Van Domselaar wrote: > > I'm not discouraged by this white paper, on the contrary, I'm happy that > other people are validating the conclusions that we have drawn. Yeah. > Here > are my (initial) thoughts on the advantages of loci of the the netgenics > model: > > 0. Loci is data independent, netgenetics in bioinformatics-centric Right. Speaking a data independence. It looks as though SYNERGY uses an internal format for their biodata, which we have decided against. An internal format requires 2 conversions between incompatible components: GENBANK 1 Internal 2 Analysis document ---> format ---> that doesn't read GENBANK The 'converter locus' scheme that Loci uses, would do only 1 conversion via the converter. > 1. Loci is free under LGPL, netget is definitely Not. Yep. > 2. We are free to use the concepts provided by netgen to evaluate and > refine our model. How free? Did you see any statement to that effect? > 3. NetGenics is vary vague about the actual client/server apps that > will plug in to their architecture Will they provide them? Will others? Hmmm. Unless they are trying to develop an open standard. > 3. Loci provides a graphical scripting language for the construction of > complex data processing systems in a 'batch' or 'pipeline' mode, the > netgenics white pages are very vague on this subject, as are they on the > status of their project. There are several innovations we have made beyond the basic framework. > maybe we'll wait and see? Maybe we will beat > them to the punch. This raises the issue of completing our design and > implementing our code. with Justin et al's work on the pyortit project, > and H. Mangalam's command line, pipeline-ready bioinformatics apps (for > designing, developing, and testing our network object model), we may be > further along with the loci network object model framework & testing > plug-in architecture than we might think. Time is of the essence. > (Jeff: it may be time to get a > global status report on loci soon anyways). Ahem. Yeah, I was planning on do something a la Gnome status report pretty soon. > 4. Netgenics will be charging big dollars for their framework, we will > be charging 0 dollars for our framework. I suppose. > 5. They will be running through Java, which IMHO sucks pretty bad. its > more example of pushing the web to places where it was not really > intended. Why is it there are so many Java apps for bioinformatics, yet no one seems to use them? > P.S. Paul Stothard (my roomate found and ad for Netgenics in Nature in > the last journal-- they may be recruiting for developers. I'mnot sure > how far beyond vaporware they are at the moment. Maybe we'll all go work for them :-) > In summary, I say we look at their proposal, also at APpLab, and we > adopt the idl protocols outlined in applap, which are largely consistent > with the OMG RFP for biomolecular proposed IDL in the OMG adoption > process (RFP for Biomolecular Sequences analysis) and when it is > adopted: We are certainly free to borrow ideas from AppLab. > from lifesciences home page: > http://www.omg.org/homepages/lsr/agendas/cambridge.html > <snip> > The Cambridge Meeting will be even more action-packed with the following > plannedactions: > Vote on recommendation to adopt Biomolecular Sequence > Analysis RFP Joint Revised Submission > Vote on recommendation to adopt Genomic Maps Joint Revised > Submission (following vote-to-vote) > Issue Clinical Trials Laboratory Data Interchange RFP > Finalize Entity Identification RFP (to be issued at the > January meeting) > Draft Cheminformatics RFP (to be issued at the January > meeting) > Draft Gene Expression RFP (to be issued at the January > meeting) > > (there is a vote in Cambridge MA on 15-19 November 1999 > </snip> Who's able to attend? Cheers. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff at bioinformatics.org | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://bioinformatics.org/ | +----------------------------+