Bioinformatics and Computational Biology Services

News

119Bowtie, bowtie2, cufflinks and velvet updated08 May 2012
Bowtie has been updated to version 0.12.8, bowtie2 to version 2.0.0beta6 and cufflinks to version 2.0.0. Velvet: users usually compile their own copy, depending on parameters.
118RepeatMasker, Repbase and stacks updated25 Apr 2012
RepeatMasker is now using the latest copy of Repbase (and was updated to the version released just after we last updated it in 2011). Stacks has been updated to version 0.9991.
117Edena, InterPro and SmolDyn updated12 Apr 2012
Edena has been updated to version 110920, the InterPro database to release 36.0 and Smoldyn to version 2.26.
116Tophat, Abyss, artemis and BEAST updated10 Apr 2012
Tophat has been updated to version 2.0.0, Abyss to version 1.3.3, artemis to version 14 and BEAST to version 1.7.1.
115BLAST, Mr Bayes, Stampy updated05 Apr 2012
BLAST has been updated to version 2.2.26+, Mr Bayes has been updated to version 3.2.1 and Stampy has been updated to version 1.0.17
114Maker updated19 Mar 2012
Maker has been updated to version 2.24
113RAxml and stampy updated29 Feb 2012
RAxml has been updated to version 7.2.8 and Stampy has been updated to release 1.0.16
112BEAST and CEGMA updated28 Feb 2012
BEAST has been updated to release 1.7 and CEGMA to version 2.4
111Tophat and Abyss updated27 Feb 2012
Tophat has been updated to version 1.4.1 and Abyss to version 1.3.2.
110Velvet updated20 Jan 2012
Velvet has been updated to release 1.2.01
109Condor upgraded20 Jan 2012
Condor has been upgraded to release 7.6.6, which fixed a fatal bug with the scheduler with 7.6.5.
108Tophat updated07 Jan 2012
Tophat has been updated to version 1.4.0.
107Condor upgraded04 Jan 2012
Condor has been upgraded to release 7.6.5.
106cufflinks updated03 Jan 2012
cufflinks has been updated to version 1.3.0.
105stampy updated21 Dec 2011
Stampy has been updated to release 1.0.14
104InterPro updated21 Dec 2011
The InterPro database has been updated to release 35.0.
103Samtools and ABySS updated14 Dec 2011
The Samtools package and the AbySS assembler have been updated
102Mr Bayes and stacks updated05 Dec 2011
Mr Bayes and stacks have been updated. See the new information and manual for Mr Bayes in the software documentation.
101analysis installed11 Nov 2011
The analysis package for evolutionary genetic analysis has been installed.
100R and Bioconductor updated09 Nov 2011
R and Bioconductor have been updated; if you need additional packages installed please ask.
99Condor upgraded08 Nov 2011
Condor has been upgraded to a major new release 7.6.4. If you condor_compile your own software then you should recompile it against the new condor libraries.
98Tophat updated31 Oct 2011
Tophat has been updated to version 1.3.3.
97Bowtie 217 Oct 2011
Bowtie 2 has been installed. Please read the manual about differences between this and Bowtie 1 (the program names differ). See links from the software page.
96EMBOSS Explorer14 Oct 2011
A link to EMBOSS 6 via EMBOSS Explorer has been added to the home page but the old version is still there in case of problems. Note that W2H is not supported.
95T-COFFEE updated14 Oct 2011
t_coffee has been updated to the latest beta version as there was a bug causing serious problems in the main release. t_coffee now invokes a wrapper that should run it correctly.
94Clustalo updated06 Oct 2011
Clustalo has been updated to version 1.0.3.
93Modeller updated06 Oct 2011
Modeller has been updated to version 9.10.
92InterPro updated06 Oct 2011
The InterPro database has been updated to release 34.0.
91RepeatScout installed21 Sep 2011
RepeatScout finds repeat families in genomes and can be used before RepeatMasker
90IMa2 and stacks updated17 Sep 2011
See relevant web sites for lists of bug fixes.
89MIRA updated12 Sep 2011
MIRA has been updated to version 3.4.
88cufflinks updated09 Sep 2011
See the software documentation for link to the web site.
87mafft updated07 Sep 2011
See the software documentation for link to the web site and see Changelog for details.
86edena updated07 Sep 2011
See the software documentation: the previous version is now edena2 and edena is now the development version 3.
85clustal updated06 Sep 2011
See the software documentation for revised program names for the current versions and clustal omega for protein sequences.
84CEGMA updated05 Sep 2011
CEGMA has been updated to release 2.3
83BEAST updated02 Sep 2011
BEAST has been updated to release 1.6.2
82InterPro updated25 Aug 2011
The InterPro database has been updated to release 33.0.
81BioPerl updated, biogrep, InStruct and SciPy installed15 Aug 2011
BioPerl has been updated and biogrep, InStruct and the Python SciPy library have been installed.
80FAR, lucy and sff_extract installed29 Jul 2011
FAR is for removing adapter sequences from sequencing reads, lucy is for cleaning sequence data and sff_extract extracts reads from 454 sff files. See software page.
79stampy installed27 Jul 2011
stampy is for mapping short Illumina reads against a reference genome and is reported as good for mapping where there are sequence variations including when reads are from divergent species. See software page.
78sff2fastq installed21 Jul 2011
sff2fastq converts between 454 and fastq formats
77Python; cgrep19 Jul 2011
A copy of Python 2.7 has been installed in /usr/local/bin so older versions are available but not the default. cgrep has been installed.
76Tophat updated23 Jun 2011
Tophat has been updated to version 1.3.1.
75Pfam updated21 Jun 2011
The Pfam database has been updated to release 25.
74IGV, Raxml, structure, t_coffee, tophat, velvet, cufflinks (again) updated03 Jun 2011
See documentation.
73Cufflinks, psipred updated31 May 2011
cufflinks and some other software is being rapidly developed: if you notice new versions please ask.
72Abyss, bayenv, consed, modeller, muscle, paml, phylobayes installed/updated27 May 2011
Some documentation has been revised
71Mafft, maker, mira updated19 May 2011
mafft now includes multithreading.
70Artemis, Augustus, Blast, Fasta, iqpnni, samtools updated17 May 2011
Artemis version 13, as for previous versions, may need options tuned for individual users. Fasta36 is a major new release with significant changes. See documentation.
69R, BioConductor and Phyml updated16 May 2011
R has been updated to version 2.13 and Bioconductor has been updated to version 2.8. Phyml has been updated and the new program phytime has been installed. There are a number of other new programs with phyml that could be installed if required.
68BamTools installed06 May 2011
BamTools has been installed; this adds to the functionality already available with SAMtools. BWA has been updated
67InterPro and other updates28 Apr 2011
The InterPro database and iprscan software have been updated. The NCBI SRA toolkit has been installed. Velvet has been updated and there is now a threaded version.
66Software updated in March31 Mar 2011
BEAST, BEST, BioPerl-Run, hyphy, samtools, smoldyn, stacks and strat were updated/installed in March.
66Software updated in February28 Feb 2011
BioPerl, iprscan, maker, Picard tools, RepeatMasker, rmblast, tophat/cufflinks were updated/installed in February.
65Software updated in January31 Jan 2011
Linkage analysis software such as genehunter, mega2, merlin, pedcheck, simwalk2 was updated or installed. Software used in genome annotation such as augustus, PASA and supporting software was also updated or installed.
64InterPro updated17 Dec 2010
The InterPro database has been updated to release 30.0.
63New software installed16 Dec 2010
Recently installed software includes TopHat, FastX-Toolkit, im, ima and ima2. See documentation
62Octave and Shogun installed29 Nov 2010
Octave (similar to Matlab) has been set up so it can be run on CamGrid. Shogun has been installed similarly. Please ask if you would like to try either of them.
61Pathway Tools installed22 Nov 2010
Pathway Tools is a systems biology software system that can integrate many datatypes from genomes to metabolic pathways.
60R and Bioconductor updated11 Nov 2010
R has been updated to version 2.12 and Bioconductor has been updated to version 2.7.
59Bowtie and cufflinks installed10 Nov 2010
Bowtie, the very fast short read aligner, and Cufflinks, for assembly and analysis of transcripts, have been installed and added to the documentation.
58Mr Bayes information05 Nov 2010
New information on running Mr Bayes has been added to the documentation. Thanks to Mark Calleja and Joel Dacks.
57InterPro updated03 Nov 2010
The InterPro database has been updated to release 29.0.
56CEGMA installed03 Nov 2010
The CEGMA pipeline to build genome annotations and check for completeness of the genome/annotations has been installed and added to the documentation.
55Condor upgraded20 Oct 2010
Condor has been upgraded to a minor new release 7.4.4. This should have fixed a bug with parallel jobs in 7.4.3.
54Velvet updated19 Oct 2010
Velvet has been updated to release 1.0.13.
53BEAST updated30 Sep 2010
BEAST has been updated to release 1.6.
52NCBI BLAST+ updated30 Sep 2010
NCBI BLAST+ has been updated to release 2.2.24 and users are strongly urged to switch from blastall (which has not been updated).
51InterPro updated07 Sep 2010
The InterPro database has been updated to release 28.0
50SAM Tools installed03 Sep 2010
SAM Tools, for for manipulating large nucleotide alignments, have been installed and added to the documentation
49Condor upgraded26 Aug 2010
Condor has been upgraded to a major new release 7.4.3. If you experience new problems with standard universe jobs you may need to re-link against the libraries in this release.
48ROADTRIPS installed; R updated23 Aug 2010
A new program for case-control association testing has been added to those available and added to the documentation.. R has been updated to version 2.11.1. R can be bundled up and run on CamGrid.
47New software22 Jul 2010
Various packages installed or updated recently have not appeared in the news and include: signalp, mitoprot, trf, Maker, bwa and Novocraft. They are now all in the documentation.
46Staden updated07 Jun 2010
The Staden package has been updated to version 2.0.0b6, including gap5 for NGS data. This is available for now with the command staden_new whereas the previous version is available with the command staden.
45Aqua updated04 Jun 2010
Aqua has been updated to version 1.1.
46InterPro updated04 Jun 2010
The InterPro database has been updated to release 27.0
45T-Coffee updated10 May 2010
T-Coffee has been updated to version 8.69.
44R and BioConductor updated05 May 2010
R has been updated to version 2.11.0 and BioConductor to version 2.6. See BioConductor 2.6 News
43NCBI nt database installed04 May 2010
The nt nucleotide database for BLAST has been installed and the description has been added to the documentation.
42Modeller updated28 Apr 2010
Modeller has been updated to version 9.8.
41Phyml on CamGrid23 Apr 2010
Phyml has been condor compiled and the revised submit script is linked to from the documentation. Local usage is unchanged.
42Picante installed19 Apr 2010
Picante is an R package for integrating phylogenies and ecology. The manual has been linked to from the documentation.
41Phylip updated14 Apr 2010
The Phylip package has been updated to version 3.69.
40Velvet updated09 Apr 2010
The Velvet sequence assembly package has been updated to version 0.7.62.
39InterPro updated08 Apr 2010
The InterPro database has been updated to release 26.0
38BLAST updated08 Apr 2010
The NCBI BLAST+ package and blastall have been updated to version 2.2.23.
37Tachyon installed01 Apr 2010
tachyon is a very fast ray tracing program. The manual has been linked to from the documentation.
36DensiTree installed22 Mar 2010
DensiTree is a program for analysing trees, eg from phylogenetic reconstructions. The manual has been added to the documentation.
35Artemis updated08 Mar 2010
Artemis has been updated to version 12.
34plink and BEAST updated05 Mar 2010
plink has been updated to version 1.07 and BEAST to version 1.5.3.
33R and BioConductor updated04 Mar 2010
R has been updated to version 2.10.1 and BioConductor to version 2.5.
32Iprscan and InterPro updated25 Feb 2010
The InterPro database has been updated to release 25.0 and iprscan has been updated to version 4.6.
31ProtTest and clumpp installed12 Feb 2010
ProtTest and clumpp have been installed and added to the documentation.
30Velvet updated04 Feb 2010
The Velvet sequence assembly package has been updated to version 0.7.57 and VelvetOptimiser.pl has been installed (replaces last update notice about 0.7.56).
29Fugue updated29 Jan 2010
Fugue has been updated to version 2.02.
28BLAST updated13 Jan 2010
The NCBI BLAST has been updated and the new BLAST+ binaries are available alongside the older versions. The documentation has a link to the BLAST+ manual.
28HMMER and Pfam updated12 Jan 2010
HMMER has been updated to version 3 and the documentation has a link to the new manual. To use version 2 invoke explicitly from /usr/bin (except hmmpfam). Pfam version 24.0 is available alongside the previous version.
27InterPro updated08 Jan 2010
The InterPro database has been updated to release 24.0.
26EMBL updated04 Jan 2010
The EMBL database has been updated to release 102. The list of included WGS datasets has been updated.
25Phyml updated09 Dec 2009
phyml has been updated to version 3.0.1 and the documentation has been changed accordingly.
24Structure updated30 Nov 2009
Structure has been updated to version 2.3.1 and the documentation has been changed.
23Standard path changed27 Nov 2009
/biosoft/bin is now before /usr/bin on the standard path for tcsh users so they will pick up and run the newer binaries we install not those with the operating system eg seaview (updated today).
22InterPro updated24 Nov 2009
The InterPro database has been updated to version 23.1
21MIRA updated23 Nov 2009
MIRA has been updated to version 3rc4
20AQUA installed23 Nov 2009
AQUA automatic quality improvment for multiple sequence software alignment installed and added to the documentation.
19inGAP installed09 Nov 2009
inGAP (Integrated Next-gen Genome Analysis Platform) has been installed and added to the documentation.
18Velvet updated05 Nov 2009
The Velvet sequence assembly package has been updated to version 0.7.55
17InterPro updated29 Sep 2009
The InterPro database has been updated to version 23.0. As we missed out version 22.0 this is the first time we have had the HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) member database, which appeared at release 22.0.
16EMBL updated24 Sep 2009
The EMBL database has been updated to release 101. The list of included WGS datasets has been updated. If you wish to have any of these kept separately please ask.
15UniProt updated10 Sep 2009
The UniProt database has been updated. This is not usually announced in this news but there was a long gap between available releases.
14BEAST updated16 Jul 2009
BEAST has been updated to version 1.4.8 (released July 2008)
13New web site15 Jul 2009
The web site has been re-written and re-styled. Please send any comments or queries you may have.
12Condor updated03 Jul 2009
Condor has been updated to version 7.2.4
11Structure and other software installed29 Jun 2009
structure, a program that implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers has been installed and added to the documentation (previously only available on cluster). A range of other software installed recently has nearly all been documented now.
10InterPro updated19 Jun 2009
The InterPro database has been updated to version 21.0.
9EMBL updated19 Jun 2009
The EMBL BLAST format database, kept in taxonomic sections, has been updated to the June 2009 release 100. The list of whole genome shotgun datasets within these data has been updated. If you want any datasets kept separately please ask.
8plink updated11 Jun 2009
The plink whole genome association analysis toolset has been updated to version 1.06
7Application form updated05 June 2009
The application form has been updated. This is for new users of the computing facilities and no longer refers to mole. If you might need a mole account please enquire (for email, web site etc).
6InterPro updated05 Jun 2009
The InterPro database has been updated to version 20.0.
5Condor updated13 May 2009
Condor has been updated to version 7.2.3. This news item replaces the one about the update to 7.2.2 as it was done immediately afterwards. Please report any problems.
4Interpro/iprscan, velvet and euler-sr updated27 Apr 2009
The InterPro database has been updated to version 19.0. The sequence assembly packages velvet and euler-sr have been updated (documentation is being revised).
3EMBL updated01 Apr 2009
The EMBL BLAST format database, kept in taxonomic sections, has been updated to the March 2009 release 99.
2Raven access to EMBOSS13 Mar 2009
You now use your Raven password to access EMBOSS via the web. However I need to register you. If you are an existing user just email me saying if you just want to use EMBOSS Explorer (does not use your own directory ie folder on the server but you can access this with Samba if required). W2H is not working reliably. You can use the link to webmaster in the footer of this page to send an email. New users should please fill in a full application form.
1Computing.bio.cam.ac.uk11 Mar 2009
The new server is open for new users. If you already have a mole account you have already been invited to ask for an account by email. If you have never had a mole account please fill in an application form. Please note the documentation and application form and so on still say mole at the moment. When time allows the form and the documentation on software etc will be revised.