SciCrunch

CTSgetR

R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Spectral Database System (SDBS)

A mass spectral database for organic compounds. The spectra included in the database are: electron impact Mass spectrum (EI-MS), Fourier transform infrared spectrum (FT-IR), 1H nuclear magnetic resonance (NMR) spectrum, 13C NMR spectrum, laser Raman spectrum, and electron spin resonance (ESR) spectrum.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

MetabolomeExpress

A metabolomics database which contains GC/MS metabolomics datasets. General users can search a curated annotated metabolite database, a metabolite response statistics database, experimental datasets, and uncurated repositories. Registered users can use Metabolome Express for data processing and management.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

mzCloud

A mass spectral database that assists in identifying compunds in life sciences, matabolomics, pharmaceutical research, toxicology, forensic investigations, environemnta analysis, food control, and industry.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Mass Spectral Library

A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Glycan Mass Spectral Database (GMDB)

A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Birmingham Metabolite Library

A collection of experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Metabolomics Society

An independent, non-profit organization whose main goal is to promote the growth and development of the field of metabolomics internationally. They also aim to provide collaborative opportunities among scientists in metabolomics, create connections between academia, government and industry in the field of metabolomics, provide opportunities for presentation of research achievements and creation of workshops, and promote the publication of meritorious research in the field.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

MetabolomeXchange

International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

MetaboLights

A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Coordination of Standards in Metabolomics

A group which aims to create open standards for metabolomics data shsaring and analysis.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Eelbrain

Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases.

Resource
SciCrunch
10 years ago - by Anonymous

Zero Mode Waveguide Imaging and Analysis package tools

MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides.

Resource
RRID-Legacy
10 years ago - by Anonymous

EVidenceModeler

Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).

Resource
RRID-Legacy
10 years ago - by Anonymous

Analysis and Annotation Tool (AAT) Package

Genome tool for analyzing and annotating large genomic sequences containing introns. It includes a program for comparing the query sequence with a protein database and another for comparing the query with a cDNA database. The database search program identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence, as well as reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region.

Resource
RRID-Legacy
10 years ago - by Anonymous

Genezilla

Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites.

Resource
RRID-Legacy
10 years ago - by Anonymous

PASA

Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.

Resource
RRID-Legacy
10 years ago - by Anonymous

Taxonomer

Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to.

Resource
RRID-Legacy
10 years ago - by Anonymous

REPCLASS

Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species.

Resource
RRID-Legacy
10 years ago - by Anonymous

RepeatScout

Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Resource
RRID-Legacy
10 years ago - by Anonymous

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