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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
Independent network and system used to collect epidemiological information for clinical research from family paediatricians in Italy. It is based on the transmission of specific data from computerised clinical files. Such data is collected anonymously by a central server in Padua, where it is validated and elaborated.
Proper citation: Pedianet (RRID:SCR_004107) Copy
http://aimlab.cs.uoregon.edu/NEMO/web/
THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Neural ElectroMagnetic Ontologies (NEMO) Project (RRID:SCR_002001) Copy
http://discover.nci.nih.gov/gominer/
GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches.
Proper citation: GoMiner (RRID:SCR_002360) Copy
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
To support Drug Development Tools development efforts, FDA established qualification programs for animal models for use under Animal Rule, biomarkers, and clinical outcome assessments. DDTs are methods, materials, or measures that have potential to facilitate drug development. Examples of DDTs may include, but are not limited to biomarker2 used for clinical trial enrichment, clinical outcome assessment used to evaluate clinical benefit, and animal model used for efficacy testing of medical countermeasures under regulations commonly referred to as Animal Rule3.
Proper citation: Drug Development Tools Qualification Programs (RRID:SCR_003714) Copy
Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.
Proper citation: FGED (RRID:SCR_001897) Copy
http://bioinformatics.biol.rug.nl/standalone/fiva/
Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) Copy
http://ftp://ftp.geneontology.org/pub/go/www/GO.tools_by_type.term_enrichment.shtml#gobean
GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible
Proper citation: GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) Copy
http://www.neuralsimulationlanguage.org/about.html
NSL, Neural Simulation Language, is a simulation system for large-scale general neural networks. NSL provides a simulation environment simplifying the task of modeling neural networks. In particular, NSL supports neural models having as basic data structure neural layers with similar properties and similar connection patterns, where neurons are modeled as leaky integrators with connections subject to diverse learning rules. Development of NSL has gone hand in hand with modeling of neural mechanisms underlying visuomotor coordination, with special emphasis on the analysis of data from anurans, monkeys, and humans. NSL follows an object-oriented design, providing higher level programming abstraction corresponding to neural elements. NSL provides system development tools, such as visualization capabilities and a run-time interpreter, which give the user powerful tools in developing and analyzing models. NSL has been widely used throughout the world for both teaching and research. simulation; software
Proper citation: Neural Simulation Language (RRID:SCR_007308) Copy
A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.
Proper citation: ALSPAC (RRID:SCR_007260) Copy
http://www.catstests.com/Product05.htm
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. CATs Card Sort is a free, general purpose card sorting program which allows the user to design sorting tasks similar to those described by Vigotsky (1934), Weigel (1941), and Grant and Berg (1948). Card sorting tasks have been shown to be particularly sensitive to frontal lobe dysfunction, but have also shown sensitivity to motor disorders, schizophrenia, chronic alcoholism, aging, and attention deficit disorder. The CATs Card Sort package provides extensive flexibility in the development of stimulus cards, allowing the experimenter to define the relevant dimensions of cards in terms of figures, letters or words, figure/letter/word color, card color, figure/letter numerosity, and a user defined dimension. Considerable flexibility is also provided in designing lists of to be sorted cards, sort criteria, and the criteria for sort classification shift. The package also provides limited analysis capabilities as described by Grant and Berg (1948). However, as with all CATs packages raw data can be copied to the clipboard in a format acceptable for import into commonly available spreadsheets such as Excel allowing the user to design analysis routines appropriate to their needs.
Proper citation: Colorado Assessment Tests - Card Sort (RRID:SCR_007331) Copy
European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases.
Proper citation: Orphanet (RRID:SCR_006628) Copy
http://comkat.case.edu/index.php?title=Home
COMKAT is a software package for compartmental modeling oriented for biomedical image quantification. Free for academic research use, COMKAT has various functions for modeling and imaging analysis in both command-line function and GUIs. COMKAT is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user.
Proper citation: Compartment Model Kinetic Analysis Tool (RRID:SCR_007359) Copy
http://www.ebire.org/hcnlab/software/cleave.html
A UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use (without loading all of the data into memory). It has been used for fMRI analysis, e.g. CLEAVE adds the following to the standard ANOVA analyses: # Unlimited numbers of factors can be analyzed. # Factor Correlation and Unequal Variance Corrections # Treatment Magnitudes: omega^2, partial eta^2, and R^2 # A convenient Ranking of Factors based upon treatment magnitudes and significance levels. # Post-Hoc Significance Tests # Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. # Allows the use of Random Factors. # A Configuration File to make the program more tunable # A Histogram and Cell Line Diagrams: which help the user to detect outliers. # Associated MATLAB functions: port CLEAVE-style data sets in or out of MATLAB.
Proper citation: CLEAVE (RRID:SCR_007113) Copy
A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options.
Proper citation: SeqExpress (RRID:SCR_007075) Copy
Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: OwlSim (RRID:SCR_006819) Copy
http://www.strokedatabase.org/pages/software.html
Diffusion tensor imaging (DTI) tractography: An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke DTI Task Card for Siemens systems, DTI Visualization platform independent tool kit, PWI analysis tools for bolus-tracking data
Proper citation: International Stroke Database/Software (RRID:SCR_007348) Copy
https://www.nitrc.org/projects/neurolabels
This resource was created to host descriptions of protocols, definitions and rules for the reliable identification and localization of human brain anatomy and discussions of best practices in brain labeling. Project for manual anatomical labeling of human brain MRI data, and the visual presentation of labeled brain images.
Proper citation: BrainColor: Collaborative Open Labeling Online Resource (RRID:SCR_006377) Copy
BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker,
Proper citation: Brain Computer Interface 2000 Software Package (RRID:SCR_007346) Copy
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