Biogang:Projects/Web applications

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Contents

Introduction

Web frameworks (Ruby on Rails, Django, Google App Engine) are increasingly popular tools to build websites. Many websites use these tools to build social networks. In science, many developers are concentrating on what has become termed (disparagingly) "Facebook for scientists". Whilst these sites can help scientists find one another and communicate, they do not (in my opinion) contribute very much to the business of doing science.


Social as in data, not social as in people

What I would like to see is less emphasis on social as in gossip and more emphasis on social as in data. By which I mean: beautifully-designed, aesthetically-pleasing, simple interfaces that allow users to:

  • deposit, view and analyse one another's data
  • if they wish, share it with their group, their department or the world at large

With all the Web 2.0 whistles and bells that we've come to expect: tagging, RSS feeds and a smattering of AJAX where appropriate.

Project Ideas

LIMS

The research world is crying out for a free, open-source, full-featured Laboratory Information Management System (LIMS) suited to the needs of small-medium labs engaged in mostly molecular biology techniques. Better still: make it social. Get your floor/department/faculty to sign up and eliminate those "does anyone have a few grams of..." emails cluttering our inboxes. It needs to handle data such as:

  • Inventories of chemicals and equipment
  • Inventories of books, manuals, protocols, SOPs
  • Contents of fridges/freezers and boxes within
  • Inventories of plasmids, bacterial strains, oligonucleotides
  • Equipment bookings
  • Cameron Neylon 07:58, 23 June 2008 (UTC):We use our lab notebook system to do a lot of this, and it could do it most of it a lot better. Planning on going into a major re-write over the summer so if people think that it could form a useful basis to work on it would be great to harness some of that effort. Conversely if people have suggestions on how to do things better or want to get in and check it out, give me a bell.
  • Mat Wood 13:51, 23 June 2008 (UTC):We have a LIMS system in place too, used to track sample production for next gen sequencing runs. It handles flexible data collection, multiple pipelines, asset management, user and equipment tracking and some basic reporting. It's written in Ruby on Rails, and we're looking to open source it soon. We hope that this can help just the small to medium scale labs you have in mind.

Structural genomics

Every SG project seems to have its own data management solution. We need a generic, modular application to handle the type of workflow generated by small-medium SG projects:

  • Target selection
  • Bioinformatic and literature analysis
  • Construct design
  • Cloning
  • Small/large scale expression
  • Protein purification
  • Crystallisation
  • Diffraction or NMR data
  • Final structure

Geodata, biology and the Google Maps API

Geotagged data is (slowly) on the rise in biology. It's always been more prevalent in areas such as ecology, conservation and environmental science but is also appearing in e.g. GSS nucleotide records from metagenome projects.

Can we devise new and useful ways to visualise these data from a "geocentric" viewpoint? Imagine a Google Maps interface to subsections of NCBI Entrez, for example?

The Wiki as software platform

In this FriendFeed conversation, we touch on the use of wikis as development environments, using extensions and plugins such as customised forms.

  • Is this a good approach to developing ELNs, LIMS etc?
  • Is anyone here actively engaged in "wiki hacking" for research tools?
  • See e.g. this presentation on WikiLims; a customised mediawiki
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