Mature open source projects are listed below. See also the brief memo on open licensing of scientific material.
rOpenGov R package ecosystem for open data and computational social science (R/GitHub) includes 20+ R packages. Introduced and NIPS Machine Learning Open Source Software workshop in 2013. Tools for Eurostat open data, Sotkanet database of National Institute for Health and Welfare (Finland), PX-web API used by the Statistical authorities in many countries, Finnish geospatial data, Finnish open government data, and other tools.
COMHIS open data analytics infrastructure of Helsinki Computational History Group. Includes tools for Finnish national bibliography, Swedish national bibliography, English Short Title Catalogue (ESTC), and Heritage of the Printed Book database (CERL).
DMT Dependency Modeling Toolkit. 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 / Waterloo Institute for Complex Systems and Innovation.
microbiome R/Bioconductor package R toolkit for microbiome analysis.
Neutral models Accelerated fitting of neutral models.
CONCOCT 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
Full agreement texts for academic publisher agreements. The agreements were released by the FinELib consortium of research libraries following our FOI request in April 2018.
Scientific journal subscription costs in Finland 2010-2017; MoE/ATT. The data set was released by Finnish Ministry of Education (Open Science and Research Initiative) following my Freedom of Information Request (summary). Finland became the first country to systematically collect and release this information.
Probiotics intervention data with high-throughput profiling of the gut microbiome and serum lipidome (RData format); from Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. Lahti et al. PeerJ 1:e32, 2013