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http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.

Proper citation: MAxEntScan (RRID:SCR_016707) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

System designed for automated collection of images from a transmission electron microscope.

Proper citation: Leginon (RRID:SCR_016731) Copy   

•   Source: SciCrunch Registry

https://dwc.tdwg.org/

Natural history collections. Offers a stable, straightforward and flexible framework for biodiversity data. Community-developed biodiversity data standard. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing identifiers, labels, and definitions. Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, samples, and related information.

Proper citation: Darwin Core (RRID:SCR_016778) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst

Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.

Proper citation: Sashimiplot (RRID:SCR_016861) Copy   

•   Source: SciCrunch Registry

https://github.com/schatzlab/genomescope

Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach.

Proper citation: GenomeScope (RRID:SCR_017014) Copy   

•   Source: SciCrunch Registry

http://pklab.med.harvard.edu/scde/pagoda.links.html

Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

Proper citation: PAGODA (RRID:SCR_017099) Copy   

•   Source: SciCrunch Registry

https://www.imicrobe.us/

Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE.

Proper citation: iMicrobe (RRID:SCR_017108) Copy   

•   Source: SciCrunch Registry

https://combine-lab.github.io/salmon/

Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.

Proper citation: Salmon (RRID:SCR_017036) Copy   

•   Source: SciCrunch Registry

https://brainlife.io/

Free cloud platform for secure neuroscience data analysis. Allows to manage data, processing and results, sharing projects privately with collaborators or publicly with brainlife.io community.Promotes engagement and education in reproducible neuroscience.You can share your neuroimaging data publicly or privately. Data on brainlife.io is organized as Datatypes to allow interoperability between Apps.

Proper citation: brainlife (RRID:SCR_020940) Copy   

•   Source: SciCrunch Registry

https://www.bcforms.org

Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.

Proper citation: BcForms (RRID:SCR_018654) Copy   

•   Source: SciCrunch Registry

https://evcouplings.org/

Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.

Proper citation: Evolutionary Couplings Server (RRID:SCR_018745) Copy   

•   Source: SciCrunch Registry

https://opensciencechain.org/

Provides data integrity using blockchain. Used for protecting integrity and provenance of research data.Open science chain utilizes distributed ledger technology (consortium blockchain) to securely store information about scientific data including its provenance to enable independent verification of its authenticity to establish trust in the research community.

Proper citation: Open Science Chain (RRID:SCR_018773) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/

Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors.

Proper citation: ANTIGENpro (RRID:SCR_018779) Copy   

•   Source: SciCrunch Registry

https://github.com/KarrLab/de_sim

Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models.

Proper citation: DE-Sim (RRID:SCR_018770) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@[email protected]

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

http://sonorus.princeton.edu/hefalmp/

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

Proper citation: Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) Copy   

•   Source: SciCrunch Registry

http://www.ornisnet.org/

ORNIS is a database of bird specimens as well as a portal to connect the academic and museum communities involved with studying birds. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Over 5 million bird specimens are housed in North American collections, documenting the composition, distribution, ecology, and systematics of the world's estimated 10,000-16,000 bird species. Millions of additional observational records are held in diverse data sets. ORNIS addresses the urgent call for increased access to these data in an open and collaborative manner, and involves development of a suite of online software tools for data analysis and error-checking. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Improved access to avian data sets will allow predictive uses to reveal patterns and processes of evolutionary and ecological phenomena that have not been apparent heretofore. Along with similar infrastructures for other vertebrate groups, it also will enable detailed and synthetic knowledge of the earth's biodiversity for tracking climate change, emerging diseases (e.g., West Nile Virus), and other conservation challenges for species in the 21st century.

Proper citation: ORNIS (RRID:SCR_002896) Copy   

•   Source: SciCrunch Registry