Projects

Sol Genomics Network

The web application that runs the Sol Genomics Network.

phylosoc2007khartmann

Conservation managers are faced with the problem of having many species that are in need of conservation but limited funds to allocate to them. This raises the question of which species should be protected. One framework for prioritising species for conservation is the Noah's Ark Problem (NAP). ... [More] The NAP combines a phylogenetic tree for the species of interest with species specific survival probabilities and conservation costs. The aim of the NAP is to allocate conservation expenditure such that future expected biodiversity is maximised. This results in a computational difficult problem -- the general problem may be NP hard -- however several algorithms have been developed by myself and others to solve variations of the NAP with particular parameter restrictions. At present no package is available that implements the various algorithms for solving the NAP. The only implementations that exist have been written for individual algorithms by a range of researchers in a range of languages. This severely restricts the application of these results to real conservation problems -- particularly as those people interested in applying these methods (eg. conservation managers) often have little mathematical or programming background. This project will implement the various algorithms for solving the Noah's Ark Problem, thereby encouraging future results to become available in the same package. A GUI will be built on top of this implementation that enables non-programmers to apply these methods and compare species prioritisations with those produced by related simple indices. This will create a common package where researchers can implement algorithms and end users can apply these results to their problems. BioPerl forms a good basis for this project as many related species specific indices are already implemented in Bio::Phylo. This project will produce species prioritisations from Bio::Tree::TreeI compatible objects and conservation information (eg. survival probabilities) using algorithms developed for solving the Noah's Ark Problem. The GUI will be cross platform deployable and easy to install. Good documentation will be produced that thoroughly describes the implemented algorithms and indices. [Less]

jperl

Various PERL scripts that I have written for processing bioinformatics data as well as general PERL subfunctions that I use. These scripts are all intended to be stand alone programs with most having a command line interface. Some of these scripts rely on the bioperl library. I use all of these ... [More] programs from the linux command line. I have all of the programs in a 'jperl' directory. I have the full path to this directory defined in my bashrc so that I can easily use them from anywhere. I am also adding a number of programs that I have written that have no other home on the web. These generally all fall under the category of bioinformatics programs. AvailabilityYou can go to the project index to see the list of all programs that are available for download. The most recent programs are available from the project source repository. [Less]

dawg-paws

THIS SITE HAS BEEN MIGRATED TO SOURCEFORGESourceforge Web SiteSourceforge Project PageProject ScriptsThe following is the previous documentation on this site. IntroductionThis is the code repository for DAWG-PAWS A Distributed Annotation Working Group Pipeline to Annotate Wheat Sequences. ... [More] DAWG-PAWS is a set of command line programs written in Perl and is released under version 3 of the GNU General Public License. Scripts in development are available for individual download at the project's subversion repository. These scripts are not all stable and are subject to change without notice. Information for downloading the entire set of scripts is available in the project's Source section. The DAWG-PAWS program assumes that you are annotating BAC sized contigs of a plant genome. The process treats each contig as a separate unit of analysis. A number of programs that may be useful a la carte include: cnv_tenest2gff.pl - Convert TE Nest output to gff format. batch_findmite.pl - Run the findmite program in batch mode. batch_mask.pl - Run the RepeatMasker program in batch mode. General Annotation SoftwareApollo - Apollo is a genome annotation curation tool. The Apollo program is the main workbench for visualizing all gff output from the DAWG-PAWS scripts. TE Annotation SoftwareFIND_LTR ltr_finder.pl FINDMITE [Less]

Gene Ontology

The Gene Ontology Consortium provides structured, controlled vocabularies and classifications that cover several domains of molecular biology and are freely available for community use in the annotation of genes, gene products, and sequences.

rnacode

rna perl analysis script rna perl analysis script rna perl analysis script

bioswf

BioSwf is an Actionscript 3 library modeled after the BioPerl and BioJava efforts. With similar intent, BioSwf classes will aid Flash developers in handling common biological data structures and tasks.

sharpton-thesis

The data and code in this repository were leveraged in the production of several comparative genomics research analyses, including an investigation of rates and mechanisms of intron gain and loss in Cryptococcus, an exploration of genome evolution in the human fungal pathogens Coccidioides, and a ... [More] fungal kingdom-wide analysis of simple sequence repeat evolution. This project was initialized by Dr. Thomas J. Sharpton from Professor John W. Taylor's lab at the University of California at Berkeley. [Less]

aligndb

AlignDB - convert genomic alignment files to an indel-concentrated database Default format is BlastZ .axt format