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

Software tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.

Proper citation: BRAINSSurfaceStats (RRID:SCR_002582) Copy   

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http://cran.r-project.org/web/packages/NanoStringNorm/

Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.

Proper citation: NanoStringNorm (RRID:SCR_003382) Copy   

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http://www.pedianet.it/en/

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   

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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   

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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   

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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   

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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   

•   Source: SciCrunch Registry

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   

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http://www.alspac.bris.ac.uk

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   

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http://www.acceleratedcure.org/index.php

A national nonprofit organization dedicated to accelerating the cure of MS by facilitating research that determines the causes and mechanisms of MS. Our main effort is the creation of a large-scale, multidisciplinary MS Repository of blood samples and data from people with MS and matched controls. We make these samples available to researchers investigating the causes of MS and other demyelinating diseases. In exchange for access to the repository, researchers agree to return the data they generate from the samples so that results from disparate experiments can be combined. We are also developing a Cure Map to establish and document what is known and what is not known about the causes of MS. From the Cure Map, Accelerated Cure Project will facilitate the research most likely to reveal the causes of MS in the shortest time through use of our MS Repository.

Proper citation: Accelerated Cure Project for Multiple Sclerosis (RRID:SCR_004743) Copy   

•   Source: SciCrunch Registry

http://gephi.org/

Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions!

Proper citation: Gephi (RRID:SCR_004293) Copy   

•   Source: SciCrunch Registry

http://ebirt.emory.edu/

Venue for research resource discovery offering resource providers a platform to advertise their services and products, as well as investigators a means to locate services for their use. Search results may be refined by resource type, research area or institution.

Proper citation: eBIRT (RRID:SCR_004172) Copy   

•   Source: SciCrunch Registry

http://www.ceinet.org/node/67

The CEI Science & Technology Network (S&TN), launched at the beginning of 2004, is composed of sevenTrieste-based research centres and their partners in the CEI region. With the aim to strengthen scientific and technological cooperation, the S&TN provides financial support for the organization of seminars, conferences, workshops and training courses. Young scientists from CEI countries, especially non-EU member States, are offered the opportunity to attend such activities and carry out scientific research on various topics in one of the seven Lead Institutions (LIs). The area of cooperation of each Lead Institution is separately defined in a three-year Protocol complemented by an annual Work Programme. During 2004-2009, the Network''s Lead Institutions implemented a number of activities, some of which in partnership with other institutions from CEI countries. This cooperation started up the Secondary Network whose further enhancement will be the main challenge in the future years. The CEI Research Fellowship Programme The CEI Research Fellowship Programme was established in 2005 to enable mobility across the CEI region by giving selected scientists the possibility of carrying out research in one of the Network''s Lead Institutions. In the time-frame 2005 - 2009, the request for fellowships has constantly increased and witnessed the effectiveness of the Programme. Taking this into account, in 2008 the CEI-ES started to explore EU funding opportunities in order to develop its Research Fellowship Programme. A joint proposal named CERES (CEI Research Fellowship Programme) was submitted to the European Commission under the Seventh Framework Programme for Research and Technological Development (FP7). CERES was approved and is currently under implementation. EU Funding opportunities for the CEI Science & Technology Network Following the successful experience of CERES, the CEI-ES, along with the Network''s Lead Institutions, will continue to look into funding opportunities offered by the EU with the ultimate aim to support mobility of researchers across the CEI area and promote significant progress in the S&T sector.

Proper citation: CEI Science and Technology Network (RRID:SCR_005338) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.seqexpress.com/

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   

•   Source: SciCrunch Registry

http://owlsim.org

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   

•   Source: SciCrunch Registry

http://www.hivebench.com/

A commercial software laboratory notebook.

Proper citation: hivebench (RRID:SCR_000915) Copy   

•   Source: SciCrunch Registry

https://www.acrobat.com/formscentral/en/

Service to create PDF and web forms.

Proper citation: Adobe FormsCentral (RRID:SCR_001729) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-genvision.aspx

A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

Proper citation: GenVision (RRID:SCR_001166) Copy   

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http://ubbmc.buffalo.edu/research/ibsos.php

Multi-center placebo-controlled randomized clinical trial to assess the short-term and long-term efficacy of cognitive behavior therapy (CBT) for irritable bowel syndrome (IBS) using two treatment delivery systems: self administered CBT and therapist administered CBT. Long term project goals are to develop an effective self-administered behavioral treatment program that can enhance the quality of patient care, improve clinical outcomes, and decrease the economic and personal costs of one of the most prevalent and intractable gastrointestinal disorders.

Proper citation: Irritable Bowel Syndrome Outcome Study (RRID:SCR_001504) Copy   

•   Source: SciCrunch Registry