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http://bioimage.ucsb.edu/bisque

Open source database for exchange and exploration of biological images. Used to store, visualize, organize and analyze images in cloud. Centered around database of images and metadata.

Proper citation: Bisque database (RRID:SCR_005559) Copy   

•   Source: SciCrunch Registry

http://carringtonlab.org/resources/cashx

Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G.

Proper citation: CASHX (RRID:SCR_005477) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/gasv/

Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

Proper citation: GASV (RRID:SCR_000061) Copy   

•   Source: SciCrunch Registry

http://www.biocheminfo.org/klotho/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry.

Proper citation: Klotho: Biochemical Compounds Declarative Database (RRID:SCR_007714) Copy   

•   Source: SciCrunch Registry

http://www3.isrl.uiuc.edu/~TeleNature/bibe/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A facility to help novices and experts find information about plants and animals in digital collections. The objectives of the Project are to facilitate access to online flora and fauna by both novices and experts through enhanced indexing, searching, and visualization techniques. Specific search facility and content will be added to help users with different levels of domain knowledge identify species based on the augmentation of professionally developed taxonomic treatments or species descriptions. This is a novel use of taxonomic descriptions.

Proper citation: Biological Information Browsing Environment (RRID:SCR_008170) Copy   

•   Source: SciCrunch Registry

http://trex.biohpc.org/

T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.

Proper citation: T-REX (RRID:SCR_010715) Copy   

•   Source: SciCrunch Registry

http://www.phenologs.org/

Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided.

Proper citation: Phenologs (RRID:SCR_005529) Copy   

•   Source: SciCrunch Registry

http://tolweb.org/tree/

A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.

Proper citation: Tree of Life Web Project (RRID:SCR_005673) Copy   

•   Source: SciCrunch Registry

http://proportal.mit.edu/

ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included.

Proper citation: ProPortal (RRID:SCR_006112) Copy   

•   Source: SciCrunch Registry

http://humanmetabolism.org/

A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format.

Proper citation: Recon x (RRID:SCR_006345) Copy   

•   Source: SciCrunch Registry

http://www.wwpdb.org/

Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.

Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy   

•   Source: SciCrunch Registry

http://arabidopsis.med.ohio-state.edu

An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB).

Proper citation: Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) Copy   

•   Source: SciCrunch Registry

http://www.agbase.msstate.edu/

A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms.

Proper citation: AgBase (RRID:SCR_007547) Copy   

•   Source: SciCrunch Registry

https://www.planetmicrobe.org/

Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data.

Proper citation: Planet Microbe (RRID:SCR_024478) Copy   

•   Source: SciCrunch Registry

https://github.com/katiasmirn/PERFect#perfect-permutation-filtering-package-in-r

Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

Proper citation: PERFect (RRID:SCR_024682) Copy   

•   Source: SciCrunch Registry

http://www.agic.umn.edu/

Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions.

Proper citation: Polar Geospatial Center (RRID:SCR_000402) Copy   

•   Source: SciCrunch Registry

https://plantcyc.org/content/plantcyc-15.2.0

Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

Proper citation: PlantCyc (RRID:SCR_002110) Copy   

•   Source: SciCrunch Registry

http://icatb.sourceforge.net/fusion/fusion_startup.php

A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

Proper citation: Fusion ICA Toolbox (RRID:SCR_003494) Copy   

•   Source: SciCrunch Registry

http://ccr.coriell.org/Sections/Collections/IPBIR/?SsId=18

The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research.

Proper citation: IPBIR - Integrated Primate Biomaterials and Information Resource (RRID:SCR_004614) Copy   

•   Source: SciCrunch Registry

http://datalad.org/

Project to adapt model of open source software distributions to address technical limitations of data sharing and develop all components of data distribution. Builds on top of git-annex and extends it with intuitive command line interface. Enables users to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. Can create DataLad datasets using any data files published on the web.

Proper citation: DataLad (RRID:SCR_003931) Copy   

•   Source: SciCrunch Registry