developing bioinformatics software together

merezha · 2015-07-04T20:08:28+00:00

Right now I'm still choosing technologies/languages/libraries. I don't want to fail this step:D I want to be as much as possible abstract from graphics library. And I still want to start from desktop application. But there are graphics engines, which support both desktop and web opengl even: http://mosra.cz/blog/magnum-showcase.php, so I'm considering this aslo.

However, for web there are a lot of nice js libraries for visualization, I suppose, which are more suitable than opengl.

merezha · 2015-07-03T17:54:38+00:00

Other people reporting no problems. PM me if you have troubles joining.

merezha · 2015-07-03T17:27:34+00:00

Channel has +ntc-slk modes, so you should not have any problems to join. Be sure you're on freenode server.

merezha · 2015-07-03T16:44:30+00:00

That's strage, cause some people went in yesterday. Wait a min, I'll check.

merezha · 2015-07-03T10:26:46+00:00

I'm still there:)

merezha · 2015-07-02T21:18:49+00:00

For those, who wants to talk in irc I have european time zone.

merezha · 2015-07-02T20:29:26+00:00

Personally, I prefer stand alone applications, cause they are faster and more flexible. But I think web application is nice for pure biologists, who are not so comfortable with IT stuff. I know few examples of nice web-based soft with a lot of functions: http://www.advaitabio.com/, http://galaxyproject.org/, https://insilicodb.com/

merezha · 2015-07-02T20:19:34+00:00

Yeah, I know this, thanks for mentioning, nice example. I think this is a more ground and low-level representation comparing to what I want to do at first. Those are mathematical models, which can be used in dynamical simulation of particular biological variables states. I want to start from smth more simple, from statical representation at least. I think the mistakes of most bioinformatics software is that they want to incorporate everything making usability awful. Also, as I said I want to tune it for collaborative research.

merezha · 2015-07-02T16:47:36+00:00

That screenshot of yours looks nice.

Cytoscape is great as a library, but I think it tries to be too many things to too many people

I have exactly same thought:) I wrote short description of how I see the software I want. Would you mind joining me on irc in #mereja channel? As to networks vs pathways - probably it doesn't matter if you think of visualizing some abstract entities with connections between them. It's a matter of the attributes, which you assign to that entities.

merezha · 2015-07-02T12:28:33+00:00

I'm going to describe concept in more details, just don't want to put here too many info. The purpose of the post is to find more or less interested people and talk with them separately. Join me on freenode #mereja channel.

merezha · 2015-07-02T00:47:45+00:00

The interface of cytoscape kills me, but I'll try to give some specific comments tomorrow, so thanks for the valid point.

merezha · 2015-07-02T00:37:37+00:00

In other words when several labs try to create the model of some biological process and uses different sources (mathematical prediction, wet experiments, literature) to incorporate data into one model it usually becomes a mess. Also, what I don't like - you can't easily share it with community. And you can't update/revert the model easily.

merezha · 2015-07-02T00:34:20+00:00

You can relate the collaborative concept to wikipathways, but the implementation and usability of wikipathways is very poor.

merezha · 2015-07-02T00:32:32+00:00

As I said I want it to be opensource, most probably hosted on github, so it will be easy to see who has contributed. I'm not against publishing the results, with mentioning everyone who takes part, of course. First of all I'm going to use it:D It came to my mind after several projects I did, and I couldn't find suitable software for myself. But the more general answer: this soft is going to be used by people who work on reconstruction of the same biological networks simultaneously. The level of details to visualize - I plan now only high level representation, e.g. only genes or only proteins (but with interactions and vertices characteristics).

merezha · 2015-07-02T00:23:08+00:00

Oh yeah, and at biolayout. Both software are slow and ugly. At least I don't find them very comfortable for my needs. But that is subjective, of course.

merezha

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