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http://www.ibioseminars.org/

iBioSeminars offers: * Free, on-demand lectures: Many universities/colleges have limited access to high profile leaders in biological research. Our goal is to add 15-20 seminars per year, of similar quality to outstanding lectures that are currently in this library. Access, through web streaming or download, is completely free-of-charge. * Targeting a broad audience: iBioSeminars start with an extended introduction, making them accessible to non-specialists and students, and then progress to cover current research. Senior scientists and students can view and enjoy these lectures. * Education: iBioSeminars are being used by undergraduate and graduate teachers to augment their classroom material. We have now added an education component to this web site (including lecture notes, questions/answers and short video clips for teaching). * International communication: iBioSeminars have viewers in 115 countries and they are being internally promoted in several countries as an educational tool and scientific resource. * Goodwill: Lecturers generously donate their time to prepare these lectures. The project, largely funded by HHMI, is a grass roots efforts with time invested by several individuals at UCSF, HHMI and ASCB.

Proper citation: iBioSeminars (RRID:SCR_005848) Copy   

•   Source: SciCrunch Registry

http://treebase.org/treebase-web/

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

Proper citation: TreeBASE (RRID:SCR_005688) Copy   

•   Source: SciCrunch Registry

http://www.plexdb.org/index.php

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.

Proper citation: PLEXdb - Plant Expression Database (RRID:SCR_006963) Copy   

•   Source: SciCrunch Registry

https://web.njit.edu/~matveev/calc.html

A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website.

Proper citation: CalC (RRID:SCR_014259) Copy   

•   Source: SciCrunch Registry

http://www.digitalfishlibrary.org/index.php

A database of 3D magnetic resonance (MRI) images of fish accessible to scientists, educators and the general public via the web. The Marine Vertebrate Collection at the Scripps Institution of Oceanography provides the majority of the DFL specimens.

Proper citation: Digital Fish Library (RRID:SCR_008338) Copy   

•   Source: SciCrunch Registry

http://interactome.baderlab.org/

Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies.

Proper citation: Human Reference Protein Interactome Project (RRID:SCR_015670) Copy   

•   Source: SciCrunch Registry

https://github.com/satijalab/seurat

Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data.

Proper citation: Seurat (RRID:SCR_016341) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/gernerlab/cytomap/-/wikis/home

Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.

Proper citation: CytoMAP (RRID:SCR_021227) Copy   

•   Source: SciCrunch Registry

https://github.com/hahnlab/CAFExp

Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.

Proper citation: Computational Analysis of gene Family Evolution (RRID:SCR_018924) Copy   

•   Source: SciCrunch Registry

http://mtshasta.phys.washington.edu/website/SuperSegger.php

Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells.

Proper citation: SuperSegger (RRID:SCR_018532) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/Drop-seq

Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.

Proper citation: Drop-seq tools (RRID:SCR_018142) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rcorrector

Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads.

Proper citation: Rcorrector (RRID:SCR_022011) Copy   

•   Source: SciCrunch Registry

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022193) Copy   

•   Source: SciCrunch Registry

http://www.geosamples.org/

Sample Catalog and Registry for the International Geo Sample Number. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search.

Proper citation: System for Earth Sample Registration (RRID:SCR_002222) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/MashMap

Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.

Proper citation: MashMap (RRID:SCR_022194) Copy   

•   Source: SciCrunch Registry

http://nsidc.org/agdc/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Archives and distributes Antarctic glaciological and cryospheric system data collected by the U.S. Antarctic Program. The Data Catalog contains data sets collected by individual investigators and products assembled from many different PI data sets, published literature, and other sources. The catalog provides useful compilations of important geophysical parameters, such as accumulation rate or ice velocity. The NSF OPP Guidelines and Award Conditions for Scientific Data state that PIs should submit data collected as a result of their OPP grant to a designated data center as soon as possible, but no later than two years after the data are collected.

Proper citation: Antarctic Glaciological Data Center (RRID:SCR_002219) Copy   

•   Source: SciCrunch Registry

http://hymao.org

A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)

Proper citation: Hymenoptera Anatomy Ontology (RRID:SCR_003340) Copy   

•   Source: SciCrunch Registry

https://github.com/chris-mcginnis-ucsf/DoubletFinder

Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.

Proper citation: DoubletFinder (RRID:SCR_018771) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

http://datasets.datalad.org/

DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.

Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy   

•   Source: SciCrunch Registry