Projects

arcanoid

A not-so-simple replication for the widely know game Arcanoid. This will be in C++ and it will be developed using Microsof's Visual Studio

Ray, a de novo assembler using MPI 2.2

de novo genome assembly is now a challenge because of the overwhelming amount of data produced by sequencers. Ray assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2 -- a message passing inferface standard.

MIA - Mapping Iterative Assembler

MIA is an reference guided assembler for DNA reads as generated by recent sequencing technologies. It is designed to support unusual short reads like they come from ancient, fragmented DNA.

est2assembly

The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data. ... [More] A Demonstration of it's capabilities can be seen at http://www.rfc.ex.ac.uk/est2assembly and http://www.insectacentral.org News8th Jan 2010Our IT departments decided to change our IP addresses on the 8th of January without considering implications on the DNS :-( As a result service to website is disrupted. Sorry about that. 11th Jan 2010Service to http://insectacentral.ex.ac.uk is restored, all others are still waiting for an IT elf to press the button... Publication is now accessible at http://www.biomedcentral.com/1471-2105/10/447 17th Jan 2010Thanks to Till for pointing out that the rfc.ex.ac.uk webpage is still down but is needed to distribute the archives. I'll try to upload them to the Google Code repository. I will have to split them to 100 Mb chunks (google restrictions) so may take a while. Really sorry about the IPs but we hope that they fix it soon... Seems though, that Google is more realiable than a University's IT department... 29th Jan 2010There is a tiny bug in the install.pl script prior release 1.02. It caused errors in the last step when copying the links: Instances of "find -L ./$installed " should become => "find -L $installed " No need to download updated tar archive for this small change. You could manually edit it or updated from CVS. Sorry and thanks. 10 Mar 2010Version 1.03 released to coicide with the MIRA3.01 hotfix. Please update est2assembly as it features a number of improvements. Bug fixes on install.pl trim_assembly.pl now uses cdhit-est (not cd-hit-est; needs to be installed) because it is much faster than a selfblast (old cd-hit-est was not fast enough). TODO: document it Added io-lib 1.12 distribution Added support for MIRA3. Please see parameterize_assembly/bin/README.Recommend you use it instead of MIRA2 Added -cdna option in Newbler (requires Newbler 2+). This may result Newbler 1 complaining and crashing. Fixed bug in prot4EST (introduced in a previous est2assembly version) which prevented ESTScan from running 10 Mar 2010oops, file 1.03 is now fixed with the following: Fixed small bug I introduced to ic_create_naming.pl (added use Bio::SeqIO on the top) [Less]