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http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

•   Source: SciCrunch Registry

https://github.com/UCSFBiomagneticImagingLab/nutmeg

Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.

Proper citation: NUTMEG (RRID:SCR_002748) Copy   

•   Source: SciCrunch Registry

https://python-elephant.org

The Electrophysiology Analysis Toolkit (Elephant) is a Python library that provides a modular framework for the analysis of experimental and simulated neuronal activity data, such as spike trains, local field potentials, and intracellular data. Elephant builds on the Neo data model to facilitate usability, to enable interoperability, and to support data from dozens of file formats and network simulation tools. Its analysis functions are continuously validated against reference implementations and reports in the literature. Visualizations of analysis results are made available via the Viziphant companion library. Elephant aims to act as a platform for sharing analysis methods across the field.

Proper citation: Elephant (RRID:SCR_003833) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/as-peak/

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

Proper citation: AS-Peak (RRID:SCR_000380) Copy   

•   Source: SciCrunch Registry

http://www.molmine.com/magma/

A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS

Proper citation: Mini Analysis Guide for Microarrays (RRID:SCR_000596) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/documentation/knime-integration/

A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.

Proper citation: TOPPAS (RRID:SCR_000533) Copy   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.org:8080/nvm/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Proper citation: NVM (RRID:SCR_000600) Copy   

•   Source: SciCrunch Registry

http://linus.nci.nih.gov./BRB-ArrayTools.html

A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.

Proper citation: Biometric Research Branch: ArrayTools (RRID:SCR_000778) Copy   

•   Source: SciCrunch Registry

http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

•   Source: SciCrunch Registry

http://www.bork.embl.de/j/

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy   

•   Source: SciCrunch Registry

http://kofler.or.at/bioinformatics/SciRoKo/

Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output.

Proper citation: SciRoKo (RRID:SCR_000941) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/university-of-colorado-at-boulder

A portal for the core labs and facilities at the University of Colorado at Boulder.

Proper citation: University of Colorado at Boulder Labs and Facilities (RRID:SCR_001054) Copy   

•   Source: SciCrunch Registry

http://www.ezbioresearch.com

A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control.

Proper citation: EZ BioResearch (RRID:SCR_001050) Copy   

•   Source: SciCrunch Registry

http://www.qub.ac.uk/schools/BioimagingCoreTechnologyUnit/NIVTA/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability.

Proper citation: Northern Ireland Virtual Tissue Archive (RRID:SCR_004452) Copy   

•   Source: SciCrunch Registry

http://discovery.hsci.harvard.edu/

An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket.

Proper citation: Stem Cell Discovery Engine (RRID:SCR_004453) Copy   

•   Source: SciCrunch Registry

http://www.trex.uqam.ca/

A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.

Proper citation: Tree and reticulogram REConstruction (RRID:SCR_004497) Copy   

•   Source: SciCrunch Registry

https://www.fieldtriptoolbox.org

Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

Proper citation: FieldTrip (RRID:SCR_004849) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~kgaulton/chaos.shtml

A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization.

Proper citation: CHAoS (RRID:SCR_005174) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hivcd/

Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage.

Proper citation: HIVCD (RRID:SCR_005201) Copy   

•   Source: SciCrunch Registry