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http://www.nitrc.org/projects/plink

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

Proper citation: PLINK (RRID:SCR_001757) Copy   

•   Source: SciCrunch Registry
  

https://www.nitrc.org/projects/nidag

An international working group dedicated to improving access to neuroimaging results in a free and open-access manner. It seeks to establish a universal coordinate database, including both past papers and future studies. Their current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, they hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships. They are interested in hearing from people who might be willing to contribute to their projects, particularly those with programming experience. The number of published neuroimaging studies is increasing rapidly and it is not feasible to read them all. If a computer database could store key information from published fMRI papers and make that information easier to search or share, this would have substantial benefits for the neuroimaging community. Projects like AMAT, Brainmap, Brede and SumsDB have started to tackle this problem. NIDAG wants to formalize and improve these databases so that they meet the needs of the neuroimaging community. Formal meta-analysis of published data is a valuable way to assess the consistency and reliability of experimental results. A database of neuroimaging results would facilitate meta-analyses, in conjunction with tools like GingerALE and Multi-level Kernel Density Analysis.

Proper citation: NIDAG: Neuroimaging Data Access Group (RRID:SCR_001674) Copy   

•   Source: SciCrunch Registry
  

http://www.researchcatalogue.esrc.ac.uk/grants/RES-149-25-1076/outputs/read/159dcb59-55e8-40bc-9e6b-f580dbdcae64

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Obesity e-Lab is a unique, secure environment for producing, sharing, communicating and finding obesity research between epidemiologists, public health researchers and social scientists. Features of e-Lab: - Tools to share: it enables social and biomedical researchers to share data, information and analytical tools for obesity research. First, it will create a portal to provide access to the platform and facilitate social networking. - Navigation tools: Second, it will generate search and navigation tools for researchers in academic, NHS or local government organizations to find data from administrative and secure data services, via social science views of health datasets, and health science views of social datasets. Within the NHS, e-Lab links records from a variety of administrative and health (and social) care sources for broadly-specified obesity research, and make pseudonymised extracts of NHS-linked datasets available via the portal. - Analytical tools: Third, it will develop analytical tools, focused on: i) easy, reliable and privacy-protecting transformation of geo-codes in health records to other geographies and area-based social and economic measures; ii) epidemiological extensions to geographical information systems; iii) growth-standardization of child obesity measures. The tool-building will employ as much existing software as possible, focusing on the provision of simple, intuitive interfaces to proven software to make it easy for social or biomedical researchers to use collaboratively.

Proper citation: National Center for e-Social Science: Obesity e-Lab (RRID:SCR_001796) Copy   

•   Source: SciCrunch Registry
  

http://www.atcc.org/

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

Proper citation: ATCC (RRID:SCR_001672) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.13/bioc/html/cqn.html

A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

Proper citation: CQN (RRID:SCR_001786) Copy   

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https://cran.r-project.org/src/contrib/Archive/PoissonSeq/

Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.

Proper citation: PoissonSeq (RRID:SCR_001784) Copy   

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http://icahn.mssm.edu/research/resources/shared-resource-facilities/in-vivo-molecular-imaging

The In-Vivo Molecular Imaging Laboratory (IMIL) is a MSSM shared resource facility serving the research community of Mount Sinai with equipment and imaging expertise. State-of-the-art bioluminescent as well as fluorescent imaging modalities are supported for in-vivo monitoring of cellular and genetic activity. Investigators are provided with cutting edge imaging technologies as well as analysis techniques. The long-term goal is to establish a comprehensive SRF for in-vivo molecular imaging using micro-MRI, micro-PET and other modalities. IMIL houses a Xenogen IVIS-200 Series imaging system with the integrated fluorescent imaging options. Simultaneous dual reporter in-vivo imaging is possible with bioluminescence and fluorescence probes. The imaging chamber has a gas anesthesia manifold that can accommodate up to 5 mice for simultaneously image acquisition. Selectable field of views allow in-plane (X,Y) imaging resolutions of up to 60-microm. Integrated spectra filters allow for the determination of signal source depth (Z). IMIL will provide data acquisition services as well as analysis. IMIL has a dedicated imaging technologist for data acquisition. Investigators will bring their prepared animal to the lab and an IMIL imaging technologist will assist in sedating the animals and acquire imaging data. Typical imaging sessions last about an hour. Certified users who are trained in the use of the software will be able to perform their own analysis at the console. Usage of the imaging device is charged by the hour ($100/hour). Structural Imaging The IVIS-200 has the built-in capability of obtaining an image of the surface topography of the animal for 2D and 3D localization. If additional true 3D imaging data is required, micro MRI is available through the Imaging Science Laboratories (ISL). Image Analysis The IVIS-200 has an integrated image acquisition and analysis software (Living Image Software 2.50). Comprehensive data quantification is possible with this software. Raw data as well as analyzed results can be electronically transferred to the investigators. Support is also available for additional image analysis such as intermodality coregistration, 3D rendering, and group statistics. Additional software packages include MedX, SPM, Brainvoyager, Analyze, and in-house developed software.

Proper citation: Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory (RRID:SCR_001785) Copy   

•   Source: SciCrunch Registry
  

http://meme-suite.org/

Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.

Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) Copy   

•   Source: SciCrunch Registry
  

http://start.sampleofscience.com

THIS RESOURCE IS NO LONGER IN SERVICE.

Free access service resource dedicated to connect researchers creating scientific samples with scientists who need samples for their experiments. With Sample of Science researchers can submit samples, or contact scientists proposing sample for dissemination. Each disseminated sample also gets its description published in Sample of Science Bulletin, a dedicated open access journal. It acquires a Digital Object Identifier (DOI) and becomes a fully citable item. Because both adequate sample descriptions and mutually-agreed dissemination conditions are key factors for a fruitful dissemination that respects mutual interest, Sample of Science provides tools to elaborate, communicate, discuss, and refine both sample description and dissemination conditions. This process, termed peer-adoption process, results in the publication of disseminated sample descriptions in Sample of Science Bulletin, a dedicated open access publication. The publication in Sample of Science Bulletin is useful to provide adequate recognition to Sample Authors who contribute to the development of science by offering visibility to their disseminated samples. To the adopter it provides experimental details regarding the sample under the form of a citable reference useful for any future publications involving this sample. To a larger scientific community interested in material science, it provides a useful tool to stay abreast the activity of sample providers in their respective field of expertise.

Proper citation: Sample of Science (RRID:SCR_001656) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/RSVSim.html

A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

Proper citation: RSVSim (RRID:SCR_001777) Copy   

•   Source: SciCrunch Registry
  

http://www.annualreviews.org/

Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields.

Proper citation: Annual Reviews: A Nonprofit Scientific Publisher (RRID:SCR_001655) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/TCC.html

An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).

Proper citation: TCC (RRID:SCR_001779) Copy   

•   Source: SciCrunch Registry
  

https://github.com/CollasLab/edd

A ChIP-seq peak caller for detection of megabase domains of enrichment.

Proper citation: Enriched Domain Detector (RRID:SCR_001693) Copy   

•   Source: SciCrunch Registry
  

https://www.clarku.edu/centers/geospatial-analytics/terrset-liberagis-features/idrisi-gis-analysis/

Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more.

Proper citation: IDRISI (RRID:SCR_001696) Copy   

•   Source: SciCrunch Registry
  

http://cshprotocols.cshlp.org/cgi/collection/behavioral_assays

A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.

Proper citation: Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays (RRID:SCR_001697) Copy   

•   Source: SciCrunch Registry
  

http://www.stat.cmu.edu/~fiasco/

Collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons.

Proper citation: Functional Image Processing software Computational Olio (RRID:SCR_001689) Copy   

•   Source: SciCrunch Registry
  

http://www.biopax.org/

Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL.

Proper citation: Biological Pathways Exchange (RRID:SCR_001681) Copy   

•   Source: SciCrunch Registry
  

http://www.brain-dynamics.net/

The Brain Dynamics Centre (BDC) is a network of centers and units. It achieves a unique exploration of the healthy brain and disorders of brain function. It translates these insights into new ways to tailor treatments to the individual. There approach is: "integrative neuroscience" - bringing together clinical observations, theory, and modern imaging technologies. And it's theoretical framework derives from linking physiology, psychology and evolution. Additionally, BDC also actively researches ADHD and conduct disorder, stress and trauma-related problems, depression and anxiety, anorexia nervosa, psychosis (including early onset) and conversion disorders. The research facilities DBC include assessment, rooms, two cognition-brain function laboratories, genotyping and an MRI Suite with 1.5 and 3T GE systems. BDC is the coordinating site for an international network - BRAINnet. It has over 180 members, and coordinates access to the first standardized database on the human brain for scientific purposes: Brain Resource International Database.

Proper citation: Brain Dynamics Centre (RRID:SCR_001685) Copy   

•   Source: SciCrunch Registry
  

https://people.cas.sc.edu/rorden/ezdicom/index.html

Software designed to display most medical images, including MRI, CT, X-ray, and ultrasound. All versions of ezDICOM can automatically detect the format of a medical image and display it on the screen. The software is easy to use, mature, and can view a wide range of medical images including proprietary formats as well as images in the DICOM standard. The software will also automatically recognize and display Analyze, GE (LX, Genesis), Interfile, Siemens (Magnetom, Somatom) and NEMA images.

Proper citation: ezDICOM (RRID:SCR_001686) Copy   

•   Source: SciCrunch Registry
  

https://protein.mpiib-berlin.mpg.de/cgi-bin/pdbs/2d-page/extern/index.cgi

The Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis.

Proper citation: Proteome 2D-PAGE Database (RRID:SCR_001678) Copy   

•   Source: SciCrunch Registry