nodalpoint.org - Linux - Comments

The people behind the

Greg — Wed, 25 Jan 2006 05:49:54 -0500

The people behind the OpenWetWare lab/project have a brainstorming page addressing many of these common concerns. The page is an excellent starting point for discussion.

Notepress

chris — Sat, 21 Jan 2006 14:42:19 -0500

I've been playing with notepress for a few days, gearing up to using it as an electronic lab book. So far, I have to say I like it. The structured blogging WP extensions come in handy too, thanks to alf's lookup hack on the journals page.

The only problem you may have here is privacy - some people may not want to blog about their work publically?

Collaborative science is

Greg — Fri, 20 Jan 2006 03:18:55 -0500

Collaborative science is still an intriguing idea and one I would like to see develop into something more substantial this year. I have been toying with the idea of inviting some of the 'bioinformatics bloggers A List' to host their weblogs on the same server as nodalpoint.

My reasoning here is that I would like to encourage the use of the structured blogging tools available for Wordpress. One way to do this would be to provide hosting and a pre-configured copy of Wordpress, with the journal paper review plug-in and Alf's Notepress extensions, to people who may actually use it. Consider it lowering the barrier to entry for anyone interested in an experimental platform for research/science/lab-notebook based blogging.

Of course you can always roll-your-own.

I would then like to aggregate paper reviews/recommendations to a central site, mix-in some tagging, FOAF, literature bookmarking from hubmed etc. and it could be the beginning of an open Faculty of 1000 or more importantly a an open collaborative science platform...

The downside of this would be the inevitable increase in bandwidth. An annual pledge fund (or advertising) may help here.

Just some thoughts, of course suggestions are welcome...

Alternatives to advertising

PedroBeltrao — Fri, 13 Jan 2006 08:34:57 -0500

There are other alternatives like a anual pledge fund for example (i would contribute :). It could also be possible to try to get a grant for Nodalpoint to develop the ideas of collaborative science or just simply to develop it further as a bioinformatics hub.

Science Blogs

Greg — Fri, 13 Jan 2006 02:33:52 -0500

PZ Myers explains the rational behind the move here.

I could see this coming: science blogging for money. I have debated running advertising on nodalpoint, however at the moment it is just not necessary. The hosting costs are modest and I just don't want to go down that road unless it is absolutely necessary. All I see is potential complications and more administrative work...

Science blogs changes

Neil — Thu, 12 Jan 2006 20:29:15 -0500

Speaking of web hosting, popular blogs Pharyngula and Stranger Fruit have migrated to a new hosting service, Science Blogs. I've changed the reading list links accordingly.

Why neither of you won't get a reply.

chris — Mon, 22 Aug 2005 00:55:52 -0400

If in doubt, read the documentation

hi ashok,i am interested in

Anonymous — Thu, 18 Aug 2005 05:39:34 -0400

hi ashok,
i am interested in the topic "Application of Linux in Bioinformatics field".
I would be grateful to receive replies regaring the above topic,
thanks in advance,
raji

prove your point

Neil — Tue, 14 Jun 2005 07:54:53 -0400

We are a tough audience here at Nodal. On the one hand, geeky enthusiasm is what we live for. On the other - if you storm in full of big promises, you'd sure better live up to them. Because we have a zero tolerance policy for bullshit.

Do not make the fatal mistake of assuming that bioinformatics is merely a branch of computer science. Because when I read claims like "analysis of almost every type of file", then I see a bunch of clustering algorithms which construct trees with nodes, I wonder how that applies to everyday bioinformatic tasks like annotating genomes or batch-processing PDB files.

Richness of data is the hallmark of biological information. I've no doubt that this software is interesting and important, but before telling me that it can do everything, take some time to understand biological problems.

complearn

cilibrar — Tue, 14 Jun 2005 05:42:38 -0400

Sure, there are many reasons details in my research papers on my homepage: http://www.cwi.nl/~cilibrar/

In summary the main reasons are
a) it's easier, usually
b) it's more robust, usually

I would like to fix the Mac OSX compile/link problems. Can anybody let me have an account for a day or two on their Mac to fix this problem? Please email me at cilibrar@gmail.com if you are up for helping.

Best regards,

Rudi

Exciting new site ?

Greg — Sun, 12 Jun 2005 23:36:36 -0400

Nodalpoint will be celebrating it's 5th anniversary in a few months. I think "exciting" rather than "exciting new" site might be a better way to put it.

So can you offer us any reason why a compression based approach is better than [insert favorite machine learning technique applied to biology here] ?

Compiling on OS X

alf — Sat, 04 Jun 2005 11:22:24 -0400

I had no luck compiling this on OS X. Things like malloc.h and -export-dynamic throw up easily fixable errors, but I wasn't able to find a way round an undefined symbol error later on.

This from Alf Eaton on Ubuntu

Greg — Thu, 17 Mar 2005 08:48:03 -0500

This from Alf Eaton on Ubuntu: certainly the closest Linux experience to OS X that I've had. That pretty much sums up my experience so far with Ubuntu. Most of the tools I use regularly on Linux are there by default which is also nice.

Distro freezes are very Debian and I've learnt to live with them, either by installing software from source, using unstable or more recently apt pinning (thanks dopey!).

As for R, self abuse is not really my thing...

Links

Neil — Mon, 22 Mar 2004 18:46:13 -0500

Their website is here. There is also a demo site for the application.

My first impression is that it looks quite useful as an alternative to submitting CLI PBS scripts, but the monitoring tools are nothing like as comprehensive or attractive as Ganglia.

Version 0.3 Recalled

Aalia Wayfare — Thu, 04 Mar 2004 21:36:51 -0500

The bioknoppix team recalled the 0.3 release on the 13th Feb due to problems with their master. They'd been trying to fix problems with jemboss.

They plan to re-release beta version 0.3 sometime next week.

I'm currently test driving it and it's clear that there are problems with the jemboss distribution. i.e. It won't launch...

If anyone intends to download it and jemboss is a key part of their attraction then I'd suggest waiting until the next release. Currently only version 0.2 is available.

They've created a mailing list for those that are interested at http://lists.hpcf.upr.edu/mailman/listinfo/bioknoppix-discuss