Bergman Lab

The Bergman Lab is committed to making all of our major software systems freely available under open-source software licenses:

• The EcologIE software from Springate and Bergman (in prep) for extracting information about species interactions from the ecological literature can be found at the project Github repository.

• The Contemplate software from Hauessler et al. (in prep.) for predicting CRMs from comparative sequence data can be found at the project SourceForge repository.

• The BioContext system from Gerner et al. (in prep) for extracting information about molecular events and their context from biomedical text can be found at the project SourceForge repository.

• The pubmed2ensembl system from Baran et al. (2011) for linking publications in PubMed to genes in Ensembl can be found at the project GitHub repository.

• The GNAT system from Hakenberg et al. (2011) for gene name normalization can be found at the project SourceForge repository.

• The text2genome system from Hauessler et al. (2011) for extracting DNA sequences from biomedical text can be found at the project SourceForge repository.

• The Gene Expression Text Miner (GETM) system from Gerner et al. (2010b) for extracting information about expression of genes in different anatomical locations from biomedical text can be found at the project SourceForge repository.

• The LINNAEUS species name recognition system from Gerner et al. (2010a) can be found at the project SourceForge repository.

• The CisPlusFinder software from Pierstorff et al. (2006) can be found at the project SourceForge repository.