Software Development

CBI-Affiliated Software

Galaxy is an open, web-based platform for data intensive biomedical research. (Goecks Lab)

GitHub is used by millions of developers to build and support projects and work together on open source techologies. (Crandall Lab)

SPAdes - St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. (Alexseyev Lab)

PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. (Crandall Lab)

TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). (Crandall Lab)

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. (Crandall Lab)

GEODIS is a program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. (Crandall Lab)

Open Tree of Life will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. (Crandall Lab)

Tree SAAP measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests. (Crandall Lab)

Software Development Tools

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.

Python is a programming language that lets you work quickly and integrate systems more effectively.

Perl is a family of languages that is a highly capable, feature-rich programming language.

R is a free software environment for statistical computing and graphics.

Software Development Information

An article about developing good open-source scientific software:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002802

An article about reproducible computational research:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285

An article about the anatomy of successful computational biology software:
http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html

An article about ten recommendations for creating usable bioinformatics command line software:
http://www.gigasciencejournal.com/content/2/1/15/abstract

An article aboutthe comparison of research in genomics to the 'Wild West':
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001744

An article about "Best Practices for Scientific Computing":
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001745

Common Workflow Language is a specification for describing analysis workflows and tools in a way that makes them portable and scalable.

LOINC provides universal codes and names that provide the global lingua franca for identifying tests and observations.

OBO Foundry aims to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. 

SNOMED is a comprehensive, multilingual healthcare terminology, used in more than 50 countries, which enables consistent, processable representation of clinical content in electronic health records.