Lab Engine Blog

Untangle the Web of Bioinformatics File Formats

admin — Wed, 22 Jul 2009 02:52:28 +0000

Looking for an easy way to deal w/ all the various sequence file formats? Does one tool output in Clustal format but you need to have the data in NEXUS format? Then check out a simple tool I’ve developed to solve that problem: Sequence Converter

Sequence Converter Website

It’s uses functionality from the BioPython framework to provide a simple way to convert from one sequence file format to another. Currently, it can read 16 different sequence formats, and output in 10 of them.

There’s also been a lot of work done on the next patch for Lab Engine, so stay tuned for further updates. And as always, let me know if you have any suggestions for new tools or features.

MeSH, Publications and More

admin — Mon, 11 May 2009 00:16:06 +0000

Aside from fixing bugs and making minor changes throughout Lab Engine, we’ve spent some time rethinking the Publications section:

Browse the MeSH terms in an interactive 3D cloud

Firstly, publications are now automatically categorized by journals, which are listed on the right side. As a new feature, we’ve also added the ability to browse the publications’ MeSH tags in an interactive cloud format. The screenshot above doesn’t do it justice, I suggest you go check it out yourself in your Lab Engine account.

The Dashboard has also gotten an overhaul: it now automatically shows recent discussions, latest application results and a list of your open tasks. Should make it easier to see at a glance what’s been going on in your various projects.

For the full patch release notes, read after the break.

General
- Dashboard now contains distinct sections for messages, files/ results and tasks
- Various design updates
- Dashboard shows the recent activities for the past 4 weeks
- Added an error page instead of the default Pylons page
- Minor graphics updates and fixes throughout Lab Engine

Publications
- List the journals instead of the ‘My publications’/ ‘Other publications’ sections
- MeSH tag cloud
- MeSH tag colors reflect project theme color

Bug Fixes
- Genome Diagram doesn’t error anymore if there aren’t any CDS features
- Publications now get deleted if no users own it
- Application result activities properly link to the lab now (for the dashboard view)
- Importing a publication from URL now works as intended
- Comment div no longer extends to the same level as the feedback form (changed float from ‘both’ to ‘left’)
- Typo fixes in Dashboard when no data is available
- Fixed typo in application listing (uploaded -> executed)

Visualizing GenBank Sequences

admin — Mon, 23 Mar 2009 05:08:33 +0000

We’ve added another visualization tool that utilizes BioPython’s GenomeDiagram API to create graphs out of GenBank sequence files. A few examples:

Circular graph

Linear graph

Currently it displays GC content and CDS features, and we’re seeking feedback on what other options to add.

Got a visualization tool you’d like to see simplified and integrated into Lab Engine? Then let me know in the comments.

Ramachandran Plot and more

admin — Mon, 16 Mar 2009 07:32:09 +0000

It’s now possible to create beautiful Ramachandran plots with a single mouse-click from within Lab Engine. All you need is a PDB file, and you’re good to go. Below is a sample output for 1ATP:

As usual, there have been numerous minor improvements that you’ll notice as you go along. And if there’s an application/ visualization you would like to see integrated, let me know in the comments.

Import Publications by DOI or URL

admin — Thu, 05 Mar 2009 01:18:04 +0000

To make it even easier to manage your publications, it is now possible to add publications to your project using a DOI or URL. (thanks to Stew for the idea) Other changes in this minor patch include bug fixes, the ability to recover account information and email notifications on important activities.

Have any other feature requests or ideas you’d like to see? Then let me know in the comments!