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http://www.plantgdb.org/

Software tools and databases for plant genomics.

Proper citation: PlantGDB (RRID:SCR_013166) Copy   

•   Source: SciCrunch Registry

http://planteome.org

An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers.

Proper citation: Planteome (RRID:SCR_014411) Copy   

•   Source: SciCrunch Registry

http://research.bioinformatics.udel.edu/iptmnet/

A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies.

Proper citation: iPTMnet (RRID:SCR_014416) Copy   

•   Source: SciCrunch Registry

http://criticalzone.org/

Data related to the National Critical Zone Observatory Program including in-situ environmental sensors, field instruments, remote sensing, and surface and subsurface imaging. The Program serves the international scientific community through research, infrastructure, data, and models. They focus on how components of the Critical Zone interact, shape Earth's surface, and support life. A primary goal is to develop high-resolution 4D datasets that inform our theoretical framework, constrain our conceptual and coupled systems models, and test our model-generated hypotheses. They are developing cross-CZO capabilities to easily share, integrate, analyze and preserve the wide range of multi-disciplinary data generated by CZOs.

Proper citation: Critical Zone Observatories (RRID:SCR_002199) Copy   

•   Source: SciCrunch Registry

http://www.marine-geo.org/portals/seismic/

Seismic Reflection Field Data from the academic research community. Their partner Academic Seismic Portal at UTIG offers additional seismic resources, http://www.ig.utexas.edu/sdc/

Proper citation: Academic Seismic Portal at LDEO (RRID:SCR_002194) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) 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

http://biosearch.berkeley.edu/

Developed as part of the BioText project at the University of California, Berkeley, the BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. The system indexes all open access articles available at PubMed Central. New articles are indexed daily. The current collection consists of more than 300 journals, 40,000 articles, 100,000 figures, and 60,000 tables. The Full Text & Abstract view searches the full text of articles (in addition to title, author, and abstract information) and returns full-text excerpts that match users' queries. Three selection boxes at the top (ABSTRACTS, FULL-TEXT EXCERPTS and FIGURES allow users to choose what the view displays. The BioText Search Engine allows users to search in tables. When the table view is selected, BioText searches in article titles, table captions, and table contents. The Grid View allows users to search over captions. It returns figures and truncated captions in a grid arrangement.

Proper citation: BioText Search Engine (RRID:SCR_003600) Copy   

•   Source: SciCrunch Registry

http://www.cise.ufl.edu/~tichen/ShapeComplexAtlas.zip

A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012

Proper citation: ShapeComplexAtlas (RRID:SCR_002553) Copy   

•   Source: SciCrunch Registry

http://clovr.org/

A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing.

Proper citation: CloVR (RRID:SCR_005290) Copy   

•   Source: SciCrunch Registry

http://total-impact.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 8, 2017. Service that aggregates altmetrics: diverse impacts from articles, datasets, blog posts, and more, to create a measure of the impact of scholarly output. * view metrics: Point to research products in Slideshare, GitHub, and Dryad. Import items from Google Scholar profiles or a BibTex file and the output is a metrics report that can be viewed and shared. * embed anywhere: Use the full-featured API to add metrics to projects. Or drop the embeddable Javascript widget into a publishing platform''s HTML. * Free - metrics data (and source code). They believe open altmetrics are key for building the coming era of Web-native science.

Proper citation: total impact.org (RRID:SCR_005952) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

http://wiki.chasmsoftware.org/index.php/Main_Page

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.

Proper citation: CHASM/SNV-Box (RRID:SCR_006445) Copy   

•   Source: SciCrunch Registry

https://github.com/raphael-group/chisel

Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers.

Proper citation: CHISEL (RRID:SCR_023220) Copy   

•   Source: SciCrunch Registry

http://biodev.ece.ucsb.edu/projects/bisquik/wiki

A scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. New features and testing of Bisque version: 0.5.1, among many others are: # Parallel execution of datasets # Rich interfaces for autogenerated module UI # Abstracted storage system for local, irods, etc.. They are using Mercurial for their source control system. This should be installed before proceeding. Browse source on-line, http://biodev.ece.ucsb.edu/projects/bisquik/browser Bisque Installation, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/InstallationInstructions05 Bisque DOWNLOAD, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/download, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bisque (RRID:SCR_005564) Copy   

•   Source: SciCrunch Registry

http://www.sb.fsu.edu/~rsref/Distribution/roadmap_distribution.htm

Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Roadmap (RRID:SCR_017207) 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

https://wholetale.org/

Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.

Proper citation: Whole Tale (RRID:SCR_017537) Copy   

•   Source: SciCrunch Registry

https://www.rosettacommons.org/home

Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Proper citation: Rosetta (RRID:SCR_015701) Copy   

•   Source: SciCrunch Registry

https://github.com/PetaVision/OpenPV

Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models. Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures.

Proper citation: PetaVision (RRID:SCR_017451) Copy   

•   Source: SciCrunch Registry