SciCrunch

NIH Metabolomics program

A US national program which supoorts the development of technologies in order to enhance the metabolomics field. It specifically increases the national metabolomics research capacity by supporting five core programs: Training in Metabolomics, Metabolomics Technology Development, Metabolomics Reference Standard Synthesis, Metabolomics Data Sharing and International Collaboration, and Comprehensive Metabolomics Resource Cores.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Metabolomics Workbench Metabolite Database

A database which contains structures and annotations of biologically relevant metabolites from public repositories such as LIPID MAPS, ChEBI, HMDB, PubChem, and KEGG. Users can search for molecular structure based on substructure, text, or mass.

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SciCrunch
10 years ago - submitted by Kristen Jensen

IUPRED

A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence.

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RRID-Legacy
10 years ago - by Anonymous

FATCAT

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.

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RRID-Legacy
10 years ago - by Anonymous

Composition Profiler

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

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RRID-Legacy
10 years ago - by Anonymous

PhyML

Web phylogeny server based on the maximum-likelihood principle.

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RRID-Legacy
10 years ago - by Anonymous

ProtTest

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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RRID-Legacy
10 years ago - by Anonymous

I-TASSER

Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.

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RRID-Legacy
10 years ago - by Anonymous

clValid

An R package which contains functions for validating the results of a clustering analysis.

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RRID-Legacy
10 years ago - by Anonymous

International Human Epigenome Consortium Data Portal

A data portal of the International Human Epigenome Consortium which provides access to comprehensive data sets of reference epigenomes relevant to health and disease. The IHEC Data Portal can be used to view, search and download data already released by different IHEC-associated projects. Data are organized by consortium, by tissue, and by assay category. Users can visualize data sets using the data grid provided or the UCSC Genome Browser.

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SciCrunch
10 years ago - submitted by Ko-Wei Lin

Big Data Bag

Software package with tools which assemble, identify, and provide access to subsets of data in a large and complex data collection workflow. The software utilities work primarily with BagIt packages that conform the BDDS Bagit and BDDS Bagit/RO profiles. JSON-LD is used to provide a standard way for linking metadata with existing ontologies and vocabularies.

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SciCrunch
10 years ago - submitted by Kristen Jensen

ProtVista

A BioJS viewer for protein sequence features.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Open Targets

A public–private initiative that supports research that provides evidence on the biological validity of therapeutic targets and that gain insight into the effectiveness of pharmacological intervention. It aims to provide a research and development framework that applies human disease. It shares its information openly.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Metapath

A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

HUMAnN

A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities.

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SciCrunch
10 years ago - submitted by Kristen Jensen

BMTagger

A tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome.

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SciCrunch
10 years ago - submitted by Kristen Jensen

SitePainter

An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Fast-Unifrac

THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. Provides a suite of tools for the comparison of microbial communities using phylogenetic information.

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SciCrunch
10 years ago - submitted by Kristen Jensen

Unifrac

THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

speciateIT

A software package for speciation of 16S sequence data.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

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