nodalpoint.org - pathway - Comments

CellDesigner performance

Duncan — Fri, 23 Nov 2007 09:25:49 -0500

Hi Akira (Funahashi) I guess its you? I was using CellDesigner 3.5.1, rendering 30-50 nodes sounds better...

Hi Duncan, Thank you for

afuna — Wed, 21 Nov 2007 16:38:14 -0500

Hi Duncan,
Thank you for your interest on SBGN, and also referring to our paper :-)
I have one question on your post above. Which version of CellDesigner did you use?
We have tuned the performance of CellDesigner on 3.1, so it want get awful performance degradation.
Although CellDesigner is not scalable enough, I think it might work for 30-50 nodes on current version
of CellDesigner (3.5.2)...

AVIS Viewer

Avi Maayan — Fri, 06 Jul 2007 10:18:53 -0400

Hi,
We developed a Google gadget viewer that implements some of the features you guys are talking about.
http://actin.pharm.mssm.edu/AVIS2
Avi

Lack of patience

Animesh — Fri, 08 Jun 2007 11:32:32 -0400

Sorry about that, open-source-software movement and particularly the repo sf.net has spoiled me.
Thanks for the email id.

Geography vs. Biology?

muskirac — Thu, 07 Jun 2007 01:36:53 -0400

What I meant by geographical maps was street maps that you can find printed versions at a Walmart. You sure can make any visualization/illustration complicated by increasing the detail level. In comparison with geographical maps, visualization of biological maps is just at its infancy. Geologists have been improving maps of Earth for hundreds of years. An accurate biological map has been available to biologists only for a few decades.

Biological Network Visualization

muskirac — Tue, 05 Jun 2007 13:39:38 -0400

SBGN is a nice start for standardization of pathway notations. I hope Dr. Kitano's group get enough funding to further grow SBGN as strong as its brother SBML.

Currently we are trying to provide stable links to individual entity pages (such as gene, enzyme, pathways) at PathCase. We managed to make the site indexable by search engines. In the next release we will hopefully get rid of dynamically generated identifiers at the URLs.

I am not sure about the maximum number of visible nodes in our applet. It mostly depends on memory size accessible by the applet. However, panning/editing the graph starts to slow down after inserting 300 nodes in a modern PC.

Reply

pkarp — Mon, 04 Jun 2007 17:29:18 -0400

Gosh, yes, ten fields to fill out! It could take a minute!

People working at IT companies who are interested in hacking on the software
in their spare time should contact us via ptools-support at ai dot sri dot com.

BioCyc scalability

pkarp — Mon, 04 Jun 2007 17:18:24 -0400

Sorry if I wasn't clear about scalability. I was not talking about speed (usually the diagram of the
full metabolic network -- the cellular overview -- downloads faster than that), but about changing
the scale of the diagram -- zooming it. The Web version cannot be scaled; the version produced by
our downloadable software can be scaled.

It's probably just a matter of time before we get to that point. We have literally hundreds of
requests for enhancements from our user community to prioritize.

BioCyc scalability

Duncan — Mon, 04 Jun 2007 08:00:35 -0400

Hi Peter, I guess its you. Thanks for reminding me of BioCyc, I'm interested in what the issues are with scalability of the web versions, do you mean it takes "two to four minutes" to load yeast metabolism in BioCyc for example. Can't you just kidnap some google engineers? They only work just down the road from you :)

Many more than one dimension

Duncan — Mon, 04 Jun 2007 07:53:09 -0400

I disagree. I wasn't just thinking of DNA, there's all the data (layers, if you like) for RNA, proteins, metabolites, enzyme kinetics etc that you might want to visualise. You already have the same four dimensions as geography, for example in environmental genomics and then you've got microscopic geography to think about as well (cellular location, compartments etc). To my mind, this makes visualising pathways very challenging, probably more so that simple geography.

The beginning

Animesh — Sat, 02 Jun 2007 05:09:17 -0400

AJAX? - No
Talented engineers? - Yes
Market opportunity - Hope so
Funding? - Hope so
Since then the algorithm has not changed much.

Very interesting

Animesh — Sat, 02 Jun 2007 05:06:11 -0400

BioCyc sounds very interesting to me [especially you have mentioned the lisp api] and I would like to use. I visited the http://biocyc.org/download.shtml page and found that there is simply too much information needed to be put in to get the software. More-over what about hackers who are affiliated to some IT company and work on Bioinformatics stuff in their spare time... should they pay the fees to hack around the BioCyc?

______________________"The Answer Lies in Genome"______________________
http://fuzzylife.org/

virtual metabolic maps

pkarp — Fri, 01 Jun 2007 19:25:28 -0400

Actually, we're much closer to this than you seem to realize.

My group's Pathway Tools software is able to automatically generate metabolic map diagrams for any organism
with a sequenced genome. These diagrams are customized to reflect the metabolism of
that organism, as opposed to the old-style metabolic charts that are mosaics across all
metabolism. Here's one in the form of a PDF for Mycobacterium tuberculosis:
http://nar.oxfordjournals.org/cgi/data/34/13/3771/DC1/2
and here's one for Caulobacter crescentus:
http://nar.oxfordjournals.org/cgi/data/34/13/3771/DC1/1
Both are mentioned in this article:
"The Pathway Tools Cellular Overview Diagram and Omics Viewer"
http://nar.oxfordjournals.org/cgi/content/full/34/13/3771

Download Pathway Tools, and you can create them yourself for any organism
you like. (http://biocyc.org/download.shtml)

Web versions of these diagrams that are unfortunately not yet scalable are available
for 260 organisms through the BioCyc query page: http://biocyc.org/server.html
Just select your organism of interest, and then click on the word Diagram in the fifth
bullet down this page, to see the diagram.

Give us 10% of Google's software development budget, and we'll be even
farther along...

What is the Google magic?

simon8duke — Fri, 01 Jun 2007 14:03:46 -0400

To make the dream come truth, shall we pray for the Google magic? Yes... No ... Maybe ...?

Wait a minute, what exactly is the magic from Google?

AJAX? - No
Talented engineers? - No
Market opportunity - Maybe
Funding? - Maybe
What else? -- It is a combination of all the four above.

Now I understand why people talking "Click Your Heels Three Times and Bow to the Google Gods" and "takes a moment to imagine a shiny, happy world where the Google geniuses offer metabolic maps."

In other words, no NIH funded projects will be able to achieve this goal; only a deep-pocketed commercial entity is able to do it.

I agree that the metabolic map or a singling map of the cell is complex, but not impossible.

Simon

Re: Biology is more complicated than Geography

lindenb — Fri, 01 Jun 2007 13:07:15 -0400

Biology more complicated than geography ? I'm not a geographer but I would say the opposite: geography has four dimensions (latitude, longitude, altitude, time) and many layers : topology, hydrography, roads, etc... Our poor genomic sequence has only one dimension, but there is still not a 'google earth-like' for genomics.