[Pipet Devel] Re: SYNERGY

J.W. Bizzaro bizzaro at bc.edu
Thu Oct 14 17:35:17 EDT 1999

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

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.


> 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

> 1.  Loci is free under LGPL, netget is definitely Not.


> 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

> 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?

                         |        J.W. Bizzaro        |
                         |  jeff at bioinformatics.org   |
                         |                            |
                         |        THE OPEN LAB        |
                         | Open Source Bioinformatics |
                         |                            |
                         | http://bioinformatics.org/ |

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