nodalpoint.org - Open Bioinformatics - Comments

User-friendly, High compatibility but low requirements

amejat — Tue, 06 May 2008 17:37:22 -0400

Hi Neil,

And thanks for your interest in the project. I fixed the mistake in "invaluable".

I also completely agree on the facts that:
- we need a free open source Laboratory Information Management System
- to be adopted, it needs to be user-friendly, cross-platform, highly compatible with existing open source solutions.

I had that in mind when I joined the eyeOS team, three years ago and I always kept it in mind during eyeOS development. And it is because eyeOS fits these needs that I really think it provides the perfect platform for a LIMS:
- For users, eyeOS provides a really intuitive and user-friendly desktop-like environment, accessible from anywhere.
- For developers, eyeOS provides a complete Toolkit and set of libraries to easily and quickly develop new eyeOS applications.
- For network manager, eyeOS has very low requirements. It only needs PHP and XML (javascript being provided by the navigator). It does NOT require a MySQL (or other) database or a Java server (such as Tomcat). For this reason, it can be installed on any basic hosting plan. However, it allows the easy integration of Flash (swf), Java applets or MySQL applications. Importantly, it constitutes a secured platform to store and share documents with a Virtual File System controlling the user access to files.

To conclude, the last but not the least, eyeOS is Free and Open Source. To my knowledge, it is unique.

I hope you will take time to discover this platform and agree with me on its potential.

Best regards,

Alexandre

www.eyeLIMS.com - Free Open Source Laboratory Information Management System powered by eyeOS

Value

Neil — Tue, 06 May 2008 02:55:35 -0400

provides an unvaluable system

*Invaluable*, surely. I hope?

I'll be interested to see how this develops: the research world is in desperate need of a quality, open-source LIMS. However, I'm concerned that this LIMS is tied to an existing product. Everyone has a web browser, but not everyone will want to sign up for eyeOS and learn how to use it. A true web application is something more like Google Documents, where you just open a page and start work.

Remember, biologists will look for any excuse not to learn how to use an application; you need to keep the entry barrier as low as possible.

A wiki-like bug-tracker?

mako — Thu, 19 Jul 2007 06:50:09 -0400

Interesting question. A bug-tracker of sorts (for "bugs" in biological analysis) might be an effective tool to use. The difficulties with such an approach are:
1. Grouping the various "bugs" into logical groups. By that I mean any biological analysis is entered as a discrete project, with a listing of bugs and solutions. The "solutions" to a given problem (er, project) may then become a new bug in that evaluation of the "solutions" need to be listed, in the context where they are most appropriate. Each "solution" may of course include other "bugs" which would need to be linked together somehow (more than what bugzilla can do, for example - a "wikified" bug tracker? Which leads to the second difficulty).
2. There should be an intuitive way of browsing for, linking to, and posting said bugs and solutions that is restricts posts to accepted categories. Which might just mean boiling down bioinformatics research to the core procedural problems and enforcing those procedural steps as categories or grouping of the "bugs". Or it might mean looking in broad terms at biological analysis. Or a division between the two implementations - a low-level focus and a high-level focus of biological analysis and research wikibug-tracker.

As a side note, you might be interested in a little project that I put online in June called "RiToJo" (http://subi.chem.ucla.edu/~mako/ritojo.html) which is a tiddlyWiki-based code snippet repository for bioinformatics. Obstensively a "rosetta stone" of code procedures between different languages for bioinformatics tasks, it really is just meant as a starting point for an electronic bioinformatics lab notebook and that's what I use it for on a thumb-drive that I carry everywhere. Of course, there's a ton of stuff in my ELN that I don't share with RiToJo and most RiToJo users (there's three at UCLA, which accounts for many of the bioinformatics students at UCLA, not counting one professor for whom I harbor distinct disdain) also don't want to allow projects from their own RiToJo version to be read by the world (and possibly get scooped in the process) and like myself are too lazy to parse out non-sensitive parts of their local RiToJo ELN and merge changes. So after attempting to organize my view of bioinformatics code into RiToJo and make it chock-full of information I lost interest in it other than, like I said, as a somewhat useful starting point for someone to download and make their own ELN (tiddlyWiki's strength is that there is no install, and no web server necessary for running it locally - it's just one html file plus any associated image files).

If you're serious about an open resource discussion, of course, then this discussion qualifies as the first "bug". How to present said information?

---

The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong, it usually turns out to be impossible to get at or repair.
�Douglas Adams

reviews would be great

Neil — Fri, 13 Jul 2007 20:26:02 -0400

Yes, that sounds good. I would like to see some kind of resource for bioinformatics methods, review of methods, examples from real research, how-tos, cookbooks. We discussed this a little in response to the Bio::Blogs special edition a while ago.

I also think the Nodal wiki is a natural repository for a lot of these things - it's set up, we know where to find it and it's relatively easy for people to create content there.

Interview

nuin — Fri, 13 Jul 2007 10:23:11 -0400

I have an interview with Dr Redfield coming to SciView where I asked about her views on Open Science. In fact there will be another new interview soon with Geneious' Alexei Drummond. Good timing maybe played a role here.

Paulo

maybe bioinformatic reviews as well ?

PedroBeltrao — Fri, 13 Jul 2007 08:49:10 -0400

What do you think about putting in bioinformatic reviews ? I did once a mini review on analysis of protein evolution and I have been thinking of writing one on domain-domain interaction predictions methods. Maybe we could collect some of the best blog content into the wiki along the way for refinement etc. I think I would still post it on the blog and just mirror it on the wiki for possible participation for others and to have a place to build up.

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 ?

announcement vs. advertisement

yogibear — Thu, 27 Apr 2006 18:09:34 -0400

I have enquired in the irc #nodalpoint channel before posting, and Neil Saunders was kind enough to get back to me and enourage me to post. Announcements, by definition, are made by the people who have developed the product, aren't they? So yes, announcements are a special form of advertisement, and yes, I am from Biomatters. However, in this case the advertisement is for a freeware product.

I have never claimed that Geneious is open source. It is freeware, but closed source. We control the platform only in so far as we are the only ones who can make new platform releases. We can not take the existing platform, which we have provided for free, back from the community.

So the community will always be free to use that platform, and to develop plugins that extend the existing freeware version of the platform. I think it should be obvious that the community benefits from this possibility. What if the Eclipse platform was freeware closed source? People could still use Eclipse productively, and develop as many plugins as they feel like.

I personally think you should really reserve your aggressions for people who try to get your money, not for people who have just given you free stuff.

Please post announcements in

Greg — Thu, 27 Apr 2006 10:03:06 -0400

Please post announcements in the forums. Also if you are from Biomatters then this is not just an announcement it is advertising, in which case please let us know. For the moment I'll give this post published status, however not to the front page.

Also, I'm curious about Biomatter's claims regarding open source. The product itself is not open source, it only provides a plug-in API ? So that means you control the platform, in which case how does the benefit the community ?

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