Collaborative Software For Lab Management ?

Question

[Austinlew]

Dear all, could you share your wisdom on how you manage the lab by using any collaborative software or web based tool which does not require too much hacking and can be easily managed by people without too much programing background.

I am interested in these aspects:

1. How to make the project plan and track the progress of each lab member.
2. Collaborative manuscript writing with SVN control.
3. File sharing among the same group people.
4. Resources management like reagent stock, machine reservation.

Thank you very much in advance,

[Giovanni M Dall'Olio]

Possible duplicate: Open Source Electronic Laboratory Notebook Software?

[Bio_X2Y]

@giovanni, this question seems to be broader, I suggest keeping it open. i'm interested to see any answers!

Answer 1

[Jarretinha]

I'm particularly fond of Plone which is a CMS built on top of Zope (it's possible to use Django instead).

Plone has already some applications in bioinformatics. Just to mention Plone4Bio uses Trac as its SCM (based on SVN). Trac is nice!

Plone is web-based and standalone (no LAMP unless you want it). Adressing your points:

1. It supports workflows that can track user contribution/progress
2. Supports web based SVN access/management
3. File sharing is also a built in feature.
4. It's easy to turn Plone into a LIMS.

Besides all that, Plone is totally written in Python and deals nicely with a plethora of databases and web resources.

You can achieve similar results with Apache Lenya. However, with much more effort. Personally, I've tried a lot of CMS/LIMS systems (Drupal, Joomla, Wikis, etc.). Plone returned the best results. It has only one big problem: very annoying to visualy customize/theming.

[Austinlew]

Jarretinha, I appreciate your answer. Plone seems interesting and fit our need I am just worry about the learning curve required to set up the system.

I also go over other thread and Open Atrium mentioned by Giovanni M Dall'Olio may also a nice choice.

[Jarretinha]

Open Atrium is written on top of Drupal, which is written in PHP. I've got a lot of restrictions with things written in PHP (even liking Drupal a lot). The learning curve to use it as a CMS is pretty much the same. Drupal requires a LAMP or similar working. I do prefer avoid server maintenance a lot. Besides that Atrium/Drupal can offer similar modules/products, including LIMS. So, it´s really a matter of preference. Both are OK.

Answer 2

[Science_Robot]

Try mashing these things together:

• Git
• Dropbox
• Basecamp
• Google Documents

Not sure about machine reservation.

[Laurent]

A shared google calendar might be useful for machine reservation.

[Austinlew]

audyyy, Thank you for your advices. However I am rather seeking an integrative platform or tool than separated ones, since the latter may bring confusion to the people here in a traditional biology lab.

Answer 3

[Jeremy Leipzig]

The LIMS stuff (Resources management like reagent stock, machine reservation) is easily done with some agile web development framework like Rails or Grails.

Answer 4

[Fred Fleche]

You can have a look at the paper related to "WIST: toolkit for rapid, customized LIMS development" published at Bioinformatics in November 2010.

http://bioinformatics.oxfordjournals.org/content/27/3/437.short?rss=1

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