Disqus - Latest Comments for pansapiens

Re: Rotamerically Induced Perturbations

pansapiens — Sun, 12 Jul 2009 21:41:12 -0000

Donnie: I noticed there are also (less well tested) wrapper scripts for NAMD in the package, along side the AMBER equivalents. I'm pretty sure NAMD is provided free of charge to academics, and may be another (cheaper) option.

Re: Getting RESTive

pansapiens — Sun, 26 Oct 2008 23:46:43 -0000

Eeekk ... reading Roy's post hasn't made me much clearer on whether I've abused the term in the past, but it's likely that I have at some point.

"I suspect a lot of people get it wrong because they read only the Wikipedia entry on the subject, which is not based on authoritative sources." - RF. <- .. that's me, after spending some time reading Roy's dissertation, I fell back on the more accessible Wikipedia version.

Re: MySocial 24x7 - Companion for FriendFeed

pansapiens — Fri, 06 Jun 2008 03:15:44 -0000

The sidebar is great, it's almost always open in my Firefox.

Two feature requests:

* Middle click to open links in a new tab (+1 to michaeltwofish's vote)
* Deal with FriendFeed "Rooms". You could do this just like the "All Friends" dropdown list, just add an equivalent for "Rooms" you are subscribed to.

Re: ResolveRef

pansapiens — Thu, 05 Jun 2008 19:15:01 -0000

Source is in SVN at Google Code ( http://code.google.com/p/resolveref/ ).

Re: A global informatics collaboratory

mndoci — Mon, 02 Jun 2008 21:07:47 -0000

Andrew,

You hit the nail on the head. My dream is to essentially create a distributed version of six hour startup, although less formal. I don't think there are enough of us co-located to do it in one place, and anyways, why keep it limited geographically. We have the tools and resources and interest to do something useful here, and like you suggest the Elsevier Challenge could be a good start. The DiSo project is my other inspiration and is along the lines of what you're talking about as well. It is up to us to prove to the community that this is possible.

I have somewhat selfish reasons to be interested as well. Inasmuch as juggling work with geekness permits, I want to start programming again and actually building things I care about, at least for fun. Such a forum is the kind of kick in the behind that could actually do the trick.

Re: A global informatics collaboratory

pansapiens — Mon, 02 Jun 2008 20:28:07 -0000

This is in response to the "biogeek" global collaboratory idea, combined with a response to your previous bursty work post.

So back in April, I took a weekend off from science related stuff and participated in a 48 hour hour solo game development competition ( Ludum Dare, http://www.ludumdare.com/ ). Essentially, anyone who wants to participate registers, the theme is announced and everyone makes a video game from scratch in 48 hours. It's extremely bursty, and a lot of fun. While there are no 'teams', everyone keeps in touch during the compo, helping each other out with technical issues, demoing beta-versions of each others games and posting updates on their journal etc.

The whole thing is tied together using existing applications; Wordpress with a voting plugin, a wiki, an IRC channel for chat ... and everyone hosts their final game entries where ever they want. So what has this got to do with biogeeks collaborating on scientific problems ? Well, maybe you can see where I'm going ... at the time it struck me that a similar thing could be achieved for some "biogeek" projects ...

I think a good way to get the ball rolling would actually be to encourage a bursty weekend on a particular project (maybe the Elsevier Grand Challenge ? ... looks like things are moving faster than I can finish my comment :) ). By using existing applications, tweaked a little to our needs, I think something could be strung together ... looks like the biogang wiki is already a good focal point ( or dare I say, a "nodalpoint" ). FriendFeed seems to be the other center. A purpose built portal would always be nicer in the long term, but I think in the short term, to "just get going right now", I think the loosely-coupled Ludum Dare style collaboration should work well enough.

Re: Google Code as a science repository

pansapiens — Thu, 22 May 2008 20:01:42 -0000

It's amazing how the little differences in the interfaces between say, Google Code and Sourceforge seem to make participation easier. They essentially have similar features, and yet one always feels a whole lot more usable than the other. There are a lot of dead (or still-born) projects on Sourceforge, and I'm sure part of the reason is the messy setup for comments/bug tracking/documentation etc. It just doesn't seem as slick and easy to get an overview of what is going on in a Sourceforge project compared with one in Google Code (or Trac). I think we will see more tech-savvy (and hopefully the not-so-savvy) scientists realizing how nicely some projects can be managed this way and jumping on board in the future.

Ever since Neil wrote about setting up Trac + SVN to manage bioinformatics projects, I've been managing a few internal projects this way and it works great. Some of these will probably move to Google Code when I've cleaned them up for pubic consumption, but I really should get into the habit of just starting these out 'in the cloud' to begin with.

Re: Wordpress issues

pansapiens — Wed, 07 May 2008 01:50:06 -0000

I did notice it went down for a little while. I had similar symptoms on my blog when I tried switching from apache2-mpm-prefork to apache2-mpm-worker , while playing with some performance tweaks. In my case, however, I think the cause was that installing apache2-mpm-worker on Debian was uninstalling the required php5 packages or something. I just decided not to mess it and revert back to apache2-mpm-prefork with the appropriate php5 packages, since I really didn't have time to troubleshoot it (ultimately it would require using FastCGI). Anyhow ... same symptoms, but different problem. Looks like you got it resolved pretty quickly anyhow.