nodalpoint.org - Administration - Comments

Impressed

Neil — Tue, 06 Jun 2006 06:31:47 -0400

A great site, I hope that it achieves its goals and concur with the other comments. This kind of endeavour really needs enthusiastic individuals to keep pushing the agenda. As we all know, it's not enough to put up a site and assume that people will follow the Google trail to your door. Hey, you can even set up an internal website geared exclusively to the needs of your group and have noone visit it. That's biologists for you :)

A few points. There are many barriers to online collaborative science and one that shouldn't be underestimated is time commitments. Many postdocs are struggling to make a career and are wary of spending time on projects peripheral to their own, even if they are enthusiastic about the concept. They also have to justify their time to bosses and funding agencies. So you're relying on people who either work in a group that's open to this kind of project or who are willing to contribute their evenings and weekends to it. I know the idea is that many hands make light work, but we all know that any rigorous bioinformatic analysis takes hours or days.

Others have pointed out that we've thrown this idea around before but it hasn't come to anything yet. I think this is partly due to inability to decide if the focus should be tool development or biological discovery. We can all agree on useful software tools that we'd like to see and that kind of collaboration is conceptually quite easy - think CVS and Sourceforge. Dividing biological analysis between group members is somewhat harder, not least because it needs to be a problem in which everyone is interested, of which everyone has some background knowledge (or the will to acquire it).

I think the Synaptic Leap concept as it stands could really work. You have problems of general interest and a hierarchical structure to the types of analysis to be done which lends itself to farming out the tasks (structural modelling, sequence analysis, biomedical statistics and so on).

I agree, some one who knows

Greg — Tue, 06 Jun 2006 00:05:12 -0400

I agree, some one who knows the area needs to think it through. No one who isn't already a malaria expert will become one over night. And likely not for the fun of it. Assuming those knowledgeable people are the proprietors of the Synaptic leap then here is my suggestion:

Put this in the context of a challenged, everyone loves a challenge right ? A bioinformatics challenge, kind of like those text mining, RNA folding, protein folding challenges. Provide an hypothesis, a data set (microarray/proteomics/interaction/structural), a question (find drug targets based on...), a suggested results format etc.

There is certainly the desire in the community to work on projects in our spare time (there is certainly diverse expertise around). Anyone who wants to harness the collective intelligence of nodalpoint just needs to pose the question in just the right way.

BTW Drupal has a distributed authentication system.

Synergies

PedroBeltrao — Mon, 05 Jun 2006 12:11:43 -0400

I am just a user but my general feeling is that Nodalpoint could be in much respects a part of Synaptic Leap, like the sub-community of bioinformatics.
I agree with Greg that it will take some volunteers to kick start this collaborative science. We have played around with the idea before but somehow it never took off. Also , like Greg says it requires some organizing center. My (current) opinion is that the collective efforts are only useful if directed by good leadership. One of the problems mentioned before is that the projects themselves have to be thought carefully by someone with knowledge in the area and usually these experts are not too keen on giving away these ideas, etc.
One possible interaction with Nodalpoint could be that whenever there is a request for IT related resources they could be cross-posted in the site for example. Also Nodalpoint members could op to become members of Synaptic Leap with some shared profile system.

First, sorry about missing

Greg — Mon, 05 Jun 2006 08:52:48 -0400

First, sorry about missing this in the submission queue. I changed the date so it would be posted at the top (and encoded your email address). Second, Synapic Leap needs a press release (this post is to short to do it justice), I suggest if anyone has not visited the site you should do so immediately. It is very much in the spirit of open source, collaborative science, Science 2.0 or whatever it is being called these days.

I would really like to see collaborative science work. Unfortunately the scientific establishment is just sooo drab that I don't see online collaboration getting popular support. I still find myself explaining the point of wikis and online communication forums to people who have just sanctioned a multi-million dollar spending spree on all the latest gadgets for an *international* proteomics biomarker discovery collaboration.

Collaborative science is going to require a group of passionate volunteers to get it started. Someone will have to play the virtual PI and department head (or head cat herder maybe). The project will need to be compelling, I think malaria has some promise in that respect. It appeals to people's compassion, using their first-world skills to help poor people (patronizing I know, but it works).

Organization will be the key: clearly describe a compelling project, outline stages, goals, sub-projects and then collaboratively discuss and split up the tasks...

As to meeting up, well, the original nodalpoint cabal was formed in Australia (myself, Neil, Chris, Dopey). We were joined by others, strangely not many from the USA (I may be wrong ?). Since then we have dispersed around the globe (after finishing PhDs/Postdocs) and unfortunately none of us landed in the Bay Area (I'm currently in Taiwan), so no go on a meet up.

Nonetheless, I would be interested in arranging an IRC meet up to discuss the same. Interested ?

As Alan suggests in the

Greg — Thu, 23 Mar 2006 00:02:53 -0500

As Alan suggests in the previous comment, the best place to ask these kinds of questions is via the SIP mailing list (I assume that is the right one ?).

zope 3.2 ?

lon1 — Wed, 22 Mar 2006 12:34:12 -0500

Is SIP running under zope3.2 ?

I am just trying to see if I can set it up running , but I got ton's of messages, and the zope instance stopped. The meaningful messages was:

ZopeXMLConfigurationError: File "/var/lib/zope3/instance/1/lib/python/sip/services/appcontainerservice.zcml", line 3.2
ConfigurationError: ('Unknown directive', u'http://namespaces.zope.org/zope', u'serviceType')

It looks like the

Thanks.

Sample Inventory Program (SIP) Answers

alanrunyan — Wed, 09 Nov 2005 10:41:33 -0500

Aaron,

Best place is to ask on the sip mailing list.

I just re-read the README documentation. Yes, if you have no clue about Zope3 and how to install software you would not have much success. There *is* some upside: There are 2 deadtree books on Zope 3!

Regarding punters i.e. online demo: you can try http://sip.houston.enfoldsystems.com with the login/password, gandalf/123

Regarding QT client, since that is being developed at SFBR and outside of Enfold Systems, I do not know. They are using it in production and it probably needs quite a bit of refactoring for general consumption.

The problem is that it takes a very long time to make software usable out-of-the-box. We are hoping to go for a grant and get the NIH to pony up money for us to create a windows installer that ships with postgresql. one click install. We are very successful with the Plone Windows installer -- as an example of ease-of-use.

Thanks for your questions,
Alan Runyan
Enfold Systems
SIP, an Open Source LIMS

SIP questions

ajeffs — Mon, 07 Nov 2005 21:32:49 -0500

Alan,

Any idea when install docs with more detail than the readme in the SIP tarball will become available? Also, any chance of Enfold setting up a demo system for punters to test without having to perform a local install? Any idea when the Qt client will be out?

Aaron.

I'm a LIMS whore too

Neil — Mon, 31 Oct 2005 22:15:53 -0500

Stew over at F & L tells us:

every bioinformatician has to code at least one LIMS in their lifetime

Bah - I hate it because it's true. This must be the new "every bioinformatician has to code at least one BLAST parser in their lifetime", now that the Bio* projects have taken care of that one.

In case anyone is wondering about MamboLIMS - I've had no time either to work on it further or to package it up as a custom Mambo install. If you're comfortable with the installation and configuration of Mambo and its components (DocMan, Simpleboard Forum and Facile Forms), package and instructions are here. It's in use in our lab and works pretty well according to my "beta testers".

a good solution

Neil — Mon, 31 Oct 2005 18:44:37 -0500

I know it's a fact of 'webmaster life' but jeez, how stupid are these people? Yeah, I'm really going to buy your product because you flooded my website with 1389 links to yours.

Anyway, I think no anonymous comments is a good idea for a medium-high traffic site with lots of users - most of whom are happy to login and contribute under their own name.

Enfold Systems employee posted article

alan runyan — Wed, 26 Oct 2005 14:19:36 -0400

I'm Alan Runyan - one of the founders of Enfold Systems. We are promoting it and looking for others places to promote Sample Inventory Program to increase awareness in the bioscience domain. It's an excellent product and one of the first large scale Zope 3 applications. Some of the technology is used by Ubuntu's backoffice system. We are really proud to announce SIP's release. We also want to ask this community for feedback on the product and how/where we can get the word out to other people who are interesting in Open Source LIMS?

And yes we are very active in the Python, Zope, and Plone communities. Thanks for the recognition. Rarely do we get positive feedback saying "oh yeah and they are contributing to these communities. Being a company in Open Source often feels lonely.

we would love feedback about the product, alan runyan

Do you use this system or do

Greg — Wed, 26 Oct 2005 03:58:21 -0400

Do you use this system or do you work for Enfold PR ?

I am aware of Enfold as a Plone spin-off company (most of the lead developers work there ?) and also being quite active in the open source community. I have no problems posting this to the front page I'm just curious who is promoting the product (company or user) ?

Drupal in Deutsch

Anonymous — Mon, 29 Aug 2005 04:56:33 -0400

[Link points to german version of Drupal: chris]
Deutsche Drupal Version Downloaden

IRC

Neil — Wed, 03 Aug 2005 02:01:41 -0400

#nodalpoint on IRC is great for a quick chat. Bear in mind that the "regulars" live in the Asia-Pacific region (GMT + 10 hours for Sydney, Taipei is a couple of hours behind), so if it's quiet, it's because we're in bed.

I use the Debian/Gnome package gworldclock to keep track of what time where for various people; there are lots of similar packages.

Projects

chris — Wed, 27 Aug 2003 20:51:51 -0400

It's actually under the projects tab, here.