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http://mendel.stanford.edu/SidowLab/downloads/MAPP/

Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAPP (RRID:SCR_010775) Copy   

•   Source: SciCrunch Registry

http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

•   Source: SciCrunch Registry

http://em3d.stanford.edu

EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam. EM3D features an integrated graphical user interface that automates most of the initial alignment and reconstruction of the tilt-series data to form a 3D volume. These functions seamlessly connect with segmentation and model-generation tools that permit the user to easily and reliably extract specific structural components from the reconstructed volume. The 3D models can then be visualized and manipulated using an extensive package of surface- and volume-rendering techniques. EM3D also provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. Altogether, EM3D facilitates the analysis of 3D cell structure at the full resolution of a reconstructed volume (2-3 nm)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EM3D (RRID:SCR_007362) Copy   

•   Source: SciCrunch Registry

http://www.jcsg.org/

The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898).

Proper citation: Joint Center for Structural Genomics (RRID:SCR_008251) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

http://dna-discovery.stanford.edu/software/rvd/

Algorithm for single nucleotide variant detection using next-generation resequencing. It estimates the error rate at each base position in the reference sequence utilizing a command-line user interface through MATLAB.

Proper citation: RVD (RRID:SCR_002635) Copy   

•   Source: SciCrunch Registry

http://stanfordnlp.github.io/CoreNLP/

A Java suite of core natural language analysis tools. It can take raw human language text input and give multiple outputs, including the base forms of words, their parts of speech, and marked up structure of sentences in terms of phrases or word dependencies. Supported languages include English, Arabic, Chinese, French, German, and Spanish.

Proper citation: Stanford CoreNLP (RRID:SCR_014778) Copy   

•   Source: SciCrunch Registry

http://receptome.stanford.edu/

HPMR is a database of human plasma membrane ligands and receptors. Users can search for ligands or receptors to reveal their pairing partners and browse through ligand or receptor families to identify ligand-receptor relationships. Users can also submit their own microarray data to perform online genome-wide online searches for paracrine/autocrine signaling systems. Survey of transcriptomes based on liganded receptome allows the discovery of paracrine/autocrine signaling for known ligand-receptor pairs in previously uncharacterized tissues or developmental stages.

Proper citation: HPMR - Human Plasma Membrane Receptome (RRID:SCR_007725) Copy   

•   Source: SciCrunch Registry

https://tma.im/cgi-bin/home.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd,2023. TMAD stores raw and processed data from Tissue Microarray experiments along with their corresponding stained tissue images. In addition, TMAD provides methods for data retrieval, grouping of data, analysis and visualization as well as export to standard formats. Researchers at the Stanford University School of Medicine and their collaborators worldwide have constructed many tissue microarrays for use in basic research.

Proper citation: Tissue Microarray Database (RRID:SCR_005527) Copy   

•   Source: SciCrunch Registry

http://www.mooneygroup.org/stop/input

STOP is a multi-ontology enrichment analysis tool. It is intended to be used to help from hypothesis about large sets of genes or proteins. The annoations used for enrichment analysis are obtained automatically applying text descriptions of genes and proteins to the NCBO annotator. Text for genes is found using NCBI entrez gene, and text for proteins is found using UniProt. The text is then run though NCBO annotator with all the available ontologies. For more information about the NCBO annotator please visit: http://bioportal.bioontology.org/ The goal of National Center for Biomedical Ontology (NCBO) is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments. This work is an expansion of the work of Rob Tirrell and others on RANSUM This probject would not be possible without the contributions of Emily Howe, Uday Evani, Corey Powell, Mathew Fleisch, Tobias Wittkop, Ari Berman, Nigam Shah and Sean Mooney An account is required.

Proper citation: STOP (RRID:SCR_005322) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/nusselab/cgi-bin/wnt/

Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Insights into the mechanisms of Wnt action have emerged from several systems: genetics in Drosophila and Caenorhabditis elegans; biochemistry in cell culture and ectopic gene expression in Xenopus embryos. Mutations in Wnt genes or Wnt pathway components lead to specific developmental defects, while various human diseases, including cancer, are caused by abnormal Wnt signaling.As currently understood, Wnt proteins bind to receptors of the Frizzled and LRP families on the cell surface. Through several cytoplasmic relay components, the signal is transduced to beta-catenin , which then enters the nucleus and forms a complex with TCF to activate transcription of Wnt target genes. Protein sequence databases, Databases of individual protein families, Metabolic and Signaling Pathways, Protein-protein interactions

Proper citation: Wnt Database (RRID:SCR_006020) Copy   

•   Source: SciCrunch Registry

https://www.hmpdacc.org/ihmp/

Provides human microbiome datasets and minimum reporting standards established by DCC, from both initial HMP-1 phase and iHMP. Offers to query and retrieve metagenomic, metatranscriptomic, human genetic, microbial culture, and many other data types from each project. Provides integrated longitudinal datasets from both microbiome and host from different cohort studies of microbiome associated conditions.

Proper citation: Integrative Human Microbiome Project (RRID:SCR_015586) Copy   

•   Source: SciCrunch Registry

https://www.gsb.stanford.edu/library

Provides resources and services to support business related research and teaching at Stanford University. As part of GSB Research Hub, helps foster scholarship, teaching, and innovation by committing to access, dissemination, creation, and preservation of information and knowledge.

Proper citation: Stanford Graduate School of Business Library (RRID:SCR_023228) Copy   

•   Source: SciCrunch Registry

http://www.benchwise.org/

Repository of peer reviews of antibodies to help scientists find the right tools fast. Researchers from schools including Stanford, Harvard, John Hopkins have contributed reviews of over 1500 antibodies. Most of these reviews contain experimental details that are hard to find in publications and yet crucial for the success of antibody usage. In addition, scientists are enabled to connect through knowledge of expertise, as members are required to use their real names and lab affiliations. BenchWise is currently open to a select list of leading research institutes and is completely free. Scientists waste over 100 hours a year on either bad antibodies or finding out the right antibody usage condition, despite the fact that someone, somewhere likely has already done the same. They want to solve this problem by enabling scientists to share their product usage knowledge. Antibody records that are documented in spreadsheets are also accepted and will be parsed into individual reviews and uploaded to save you time.

Proper citation: BenchWise (RRID:SCR_006364) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/rna-viz-proto

A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion.

Proper citation: ToRNADo (RRID:SCR_002706) Copy   

•   Source: SciCrunch Registry

http://simbios.stanford.edu/index.html

Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.

Proper citation: Simbios (RRID:SCR_004320) Copy   

•   Source: SciCrunch Registry

http://parkinsons.stanford.edu

A patient resource to provide Parkinson's disease patients and their families with information and resources to help understand and manage Parkinson's disease and improve the quality of life for both patient and caregiver, while increasing public awareness about the disease. The website also connects users with resources, such as therapy groups, physical exercise classes, and patient care resources. It gives users access to mailing lists, support group information, and other Parkinson's-related event information for Parkinson's patients and their families. Based at Stanford University Medical Center, it is a partnership between the American Parkinson Disease Association, Inc. and Stanford University.

Proper citation: American Parkinson's Disease Association Information and Referral Center (RRID:SCR_013375) Copy   

•   Source: SciCrunch Registry

http://www.thechiselgroup.org/jambalaya

Jambalaya is a plug-in created for Protg which uses Shrimp to visualize the knowledge bases the user has created. Protg is an ontology editor and a knowledge-base editor which allows domain experts to build knowledge-based systems by creating and modifying reusable ontologies and problem-solving methods.

Proper citation: Jambalaya (RRID:SCR_013562) Copy   

•   Source: SciCrunch Registry

https://www.readcube.com

A software resource application which organizes research literature. Users can import PDF articles into the application and create a searchable library. ReadCube enables users to perform keyword searches and provides references as well as note-taking tools. ReadCube also recommends articles to users based on library contents. For publishers, ReadCube enables interactive PDF versions of articles with tools for readers to make notes or perform author and keyword searches.

Proper citation: ReadCube (RRID:SCR_013777) Copy   

•   Source: SciCrunch Registry