Research software impact

Scientific Open Source Software

Links to mature computational software projects, typically including multiple individual packages. Further bleeding edge development code see GitHub. All implementations come with an open source license (see the brief memo on open licensing of scientific material for recommendations).

Digital Humanities and Computational Social Science

rOpenGov R package ecosystem for open data and computational social science (R/GitHub). Introduced and NIPS MLOSS workshop 2013. Tools for Eurostat open data, Sotkanet demographic indicator database, PX-web API used by the Statistical authorities in many countries), Finnish geospatial data, Finnish open government data, Finnish national bibliography, and English Short Title Catalogue (ESTC), and other tools.

Datavaalit Parliamentary monitoring and data sharing infrastructure for Finnish election and parliamentary data. Funded by Sitra 2012-2013. Double-winner of the Apps4Finland 2012.

Machine Learning and ecological models

DMT Probabilistic tools for dependency analysis between multiple data sources (R/CRAN). Probabilistic PCA, factor analysis, CCA, regularized variants, dependency-based dimensionality reduction etc. ICML/MLOSS workshop, Israel 2010.

earlywarnings Methods for identification of critical transitions between ecosystem states from time series data (CRAN). Co-developer. CRAN/Github. WICI Data Challenge 2013 runner-up award from Waterloo Institute for Complex Systems and Innovation!

Microbial Ecology and Network Analysis

microbiome R/Bioconductor package R toolkit for microbiome analysis.

Tutorial collection for microbiome analytics

Neutral models

Metagenomic contig binning

netresponse Modeling context-specific activation patterns in genome-wide interaction networks (R/Matlab). Originally applied to study transcriptional responses in genome-scale interaction networks across organism-wide collections of gene expression data. doi:10.18129/B9.BIOC.NETRESPONSE

Functional Genomics

RPA (R/Bioconductor). Scalable probabilistic method for preprocessing short oligo microarray data. NAR 2013. doi:10.18129/B9.BIOC.RPA

pint Probabilistic data integration for DNA/RNA data in functional genomics (R/Bioc). MLSP 2009.

intcomp Benchmarking for integrative cancer gene discovery algorithms. Briefings in Bioinformatics 2012

This material is Open Knowledge