July 21st, 2009
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.
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May 10th, 2009
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.
Read the rest of this entry »
Tags: mesh, patch, publications
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March 22nd, 2009
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.
Tags: feature, genbank, visualization
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March 15th, 2009
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.
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March 4th, 2009
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!
Tags: feature, publications
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