nodalpoint.org - Open source software - 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.

Sure

nuin — Wed, 15 Aug 2007 07:48:40 -0400

The more the better.

I am in the process of finishing a manuscript and we will start coding as soon as I finish it. I send you an email with the idea.

BTW, pretty nice application you have.

Paulo

Need some help guys?

bosco — Wed, 15 Aug 2007 03:03:43 -0400

I'd love to help out even though I'm just a structural biologist and not a sequence jockey.

I have experience programming in C++/wxWidgets: I've written a complete GUI application in that platform http://boscoh.com/ramaplot. My main platform @work is Python so I'm keen to seen how wxPython stacks up against wxWidgets.

I can help you work on the GUI aspect.

what is LSID

dalloliogm — Tue, 07 Aug 2007 06:32:37 -0400

If LSID is just another 4 letter acronym to you there is more information available at http://www-124.ibm.com/developerworks/oss/lsid/

Maybe it's explained better here:
- http://lsids.sourceforge.net/
- http://www.ibm.com/developerworks/opensource/library/os-lsidbp/

more on pathways

vndinu — Sat, 16 Jun 2007 17:45:22 -0400

Interesting comments, some of the commercial pathway analysis tools are indeed quite good. I'm also working on a pathway-based analysis of genotype data, the paper is in press in the Journal of Biomedical Informatics and the tool will be made publicly available soon. valentin dinu, http://www.dinuinformatics.info

Content

alf — Thu, 19 Apr 2007 05:34:45 -0400

If you can define more precisely the types of content you'll want to log, that would make it easier to point to useful plugins/modules.

use a blog to follow a project of bioinformatics

dalloliogm — Wed, 18 Apr 2007 09:18:02 -0400

I would like to do the same thing as you with notepress: use a blog to follow a project of bioinformatics.

I'm a last-year degree student and I have to follow a short period of practice of six-months in a research laboratory; the project I will work on is an analysis of the secundary structure of some genes in yeast.
Since I'm fond of Internet and the web 2.0 stuff, my head laboratory agreed to let me work slower on my project, allowing me to spend more time on deciding how to organize it and how to present it.
I've also had had to present a seminar a few weeks ago, you can find it here: http://genome.imim.es/~giovanni/ .

so I'm trying with a wordpress blog running on my local computer: I'm using it to collect all the resources on Internet, the workflows I'm using and to take note of the progresses I make.
Actually I'm not very good with the technical part, as I'm not sure I've understood very well what COinS is and I've not tried Drupal yet (I will study ;) ).

So I was looking for some interesting plugins for wordpress: in particular, I would like to find something to manage reviews on articles and resources on Internet, and maybe to implement a connotea/citeulike/other(zotero when it will have social bookmarking utilities?) account, but I believe I won't find very much :(

What kind of thing are you

alf — Tue, 17 Apr 2007 05:13:20 -0400

What kind of thing are you trying to do? There's a COinS plugin for Wordpress that does a little bit of this, but it's not proper structured blogging. You might be better off using Drupal and defining your own CCK content types.

Structure Blogging Plugin

dalloliogm — Mon, 16 Apr 2007 10:43:15 -0400

Hi,
I was trying out this plugin, but it seems that it doesn't work anymore, it is not compatible with wordpress 2.1 and the developers aren't going to continue it (http://mail.structuredblogging.org/mailman/private/structuredblogging-di...).

Moreover, the page referred for the other plugin Notepress, is not avaible any more http://projects.hubmed.org/track/notepress :(

---

http://genome.imim.es/~giovanni

Pathway analysys and discovery

thex-raykid — Sun, 21 Jan 2007 18:04:34 -0500

It's an old discussion but it still comes out on google search...
I was recently trying to find good pathway analysis software (preferably free), reviews or anything. What I found interesting is DAVID, which is not really pathway analysis soft but quite useful tool anyway, and Pathway Discovery site with some great tips. Hope this helps.

gene wiki in ucsc

maximilianh — Fri, 27 Oct 2006 10:05:29 -0400

only a wiki that will be used by biologists will be successful in the end, in my opinion. I smell overengineering for all things set up for research purposes in the small corner of the bioinformatics community, whatever nice functionality they may have offer. I've recently discovered on the ucsc wiki that the UCSC group plans to add a "wiki track" to its highly popular genome browser. To me, this looks like a cool idea, as most people are working with these browsers all the time anyways and they sooner or later stumble upon the wiki annotations, comment on them, get angry, whatever, but it's a simple solution that people eventually might start to use one day...

Control Freaks

ejain — Thu, 19 Oct 2006 10:04:55 -0400

I'm also surrounded by control freaks, but none of these people would mind if one or more Wikis would allow people to attach data and comments to the "authoritative" version of the data. Such feedback would be very much welcome, and much of it would even be integrated back into the official version of the data. The tricky bit with this kind of setup would be to get the synchronization right: Don't want to fork the data, but can't spend a lot of time cleaning up the Wiki to take changes into account, either.

Not only concepts

leechuck — Thu, 19 Oct 2006 09:28:46 -0400

Hi,

Yes, I work with the group developing the BOWiki. My main interest there is to use a semantic wiki for collaborative ontology curation, so I am a bit biased towards its application in this field. But the idea behind the BOWiki goes beyond editing ontologies.

The main application is indeed supposed to be the annotation of genes or related biological data (yes, this data is still missing in the wiki). The idea is that people should be able to categorize genes, search or browse through them by other means than their name. One possibility to do this is to use some of the biomedical ontologies and use their annotation or let people annotate to the concepts in these ontologies. GO is one of these ontologies, and there are others. And in the BOWiki prototype, these ontologies are only present for annotation, and are not supposed to be edited. If the need arises to modify a concept in some ontology, or add a new one, then this should be possible in a wiki (you would not want to wait until changes are made official before you edit a wiki page). But then you create a new concept, which structures the content of the wiki, and do not change the GO. As you say, this concept could at some point be taken into GO, but this is not mandatory.

BOWiki is more or less a research prototype. But its goal appears to be close to the goal of other gene wiki projects. If a collaboratively curated knowledge base of gene functions is to become reality, I believe it best to have one united effort which reflects the views and needs of a wide variety of users. This is probably not BOWiki, but some of its ideas may be of use in other approaches for gene wikis, or maybe in one collaborative effort to create a gene (function) wiki. This is the reason I wrote the blog entry here.

Are you behind the BIOWIKI

Greg — Thu, 19 Oct 2006 05:54:48 -0400

Are you behind the BIOWIKI project ? Googling your username leads me to this page, and your name is listed on the project members page ?