Software License / Cost:
GNU General Public License / Free
Brief Description:
GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language. Continue Reading
TensorFlow is an open source software library for numerical computation using data flow graphs
When entering the University’s datacenter, it’s natural to wonder about the seemingly infinite sources of information being computed there. Could these systems be performing cutting-edge thermodynamic modeling? Or, perhaps are they helping to unravel some of the mysteries of quantum chemistry? That said, would your curiosity would change if the source of this data were closer to home? In fact, it’s much closer to home: the US Census Bureau or the Social Security Administration.
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About Research Computing Colloquies
These sessions will explore how computing resources help researchers take on new and greater computational tasks, enhance research productivity, increase the competitiveness of grant submissions, and advance scientific discovery across many disciplines.
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Gaussian is used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Continue Reading
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Continue Reading
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. The selection of trimming steps and their associated parameters are supplied on the command line. It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp’ed FASTQ. Continue Reading
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124 (http://www.biomedcentral.com/1471-2105/12/124). To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (manuscript in preparation), is already build in Proteinortho. Continue Reading
Orthology is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.
