Tools   Select Another Resource Report Type

http://www-is.biotoul.fr

Database of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided.

Proper citation: ISFinder (RRID:SCR_003020) Copy   

•   Source: SciCrunch Registry
  

http://spine.rutgers.edu/microarray/

Database which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip.

Proper citation: Gene Expression Profiling in Spinal Cord Injury (RRID:SCR_003260) Copy   

•   Source: SciCrunch Registry
  

http://researchmaps.org/

UCLA based service for research planning aimed to help users integrate and summarize large amounts of information into a searchable graphic format. The interactive features facilitates planning during writing of grants, research papers and reviews. ResearchMaps can also be used as a collaborative tool and as a catalyst for the creative process.

Proper citation: ResearchMaps (RRID:SCR_003178) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/IXNO

Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.

Proper citation: Interaction Ontology (RRID:SCR_003055) Copy   

•   Source: SciCrunch Registry
  

http://www.geb.uma.es/mauds

We define a simple method to detect cortical states that can be applied in real time for offline processing of large amounts of recorded data on conventional computers. Also, the online detection of up and down states will facilitate the study of cortical dynamics. An open-source MATLAB toolbox, and Spike 2-compatible version are made freely available. Intracellular recordings from different areas of the cerebral cortex were obtained from both in vitro and in vivo preparations during slow oscillations. A method that separates up and down states recorded intracellularly is defined and analyzed here. The method exploits the crossover of moving averages, such that transitions between up and down membrane regimes can be anticipated based on recent and past voltage dynamics. We demonstrate experimentally the utility and performance of this method both offline and online, the online use allowing to trigger stimulation or other events in the desired period of the rhythm. This technique is compared with a histogram-based approach that separates the states by establishing one or two discriminating membrane potential levels. The robustness of the method presented here is tested on data that departs from highly regular alternating up and down states. The neuronal cortical network generates slow (<1 Hz) spontaneous rhythmic activity that emerges from the recurrent connectivity. This activity occurs during slow wave sleep or anesthesia and also in cortical slices, consisting of alternating up (active, depolarized) and down (silent, hyperpolarized) states. The search for the underlying mechanisms and the possibility of analyzing network dynamics in vitro has been subject of numerous studies. This exposes the need for a detailed quantitative analysis of the membrane fluctuating behavior and computerized tools to automatically characterize the occurrence of up and down states.

Proper citation: MAUDS (RRID:SCR_003175) Copy   

•   Source: SciCrunch Registry
  

http://www.plexon.com/products/map-software

A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP Control Computer with the purchase of any MAP System. As the MAP System has been replaced by the advanced OmniPlex D Neural Data Acquisition System, Plexon is no longer developing the RASPUTIN software program.

Proper citation: MAP Software (RRID:SCR_003170) Copy   

•   Source: SciCrunch Registry
  

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

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry
  

http://www.compucell3d.org/

Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior.

Proper citation: CompuCell3D (RRID:SCR_003052) Copy   

•   Source: SciCrunch Registry
  

http://hugenavigator.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed.

Proper citation: HuGE Navigator - Human Genome Epidemiology Navigator (RRID:SCR_003172) Copy   

•   Source: SciCrunch Registry
  

http://www.brenda-enzymes.org/

Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB.

Proper citation: BRENDA (RRID:SCR_002997) Copy   

•   Source: SciCrunch Registry
  

http://www.tongji.edu.cn/~zhanglab/DiNuP/

Software that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. It provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise.

Proper citation: DiNuP (RRID:SCR_003046) Copy   

•   Source: SciCrunch Registry
  

http://www.coriell.org/

Non-profit research center dedicated to the study of the human genome. Expert staff and pioneering programs in the fields of personalized medicine, cell biology, cytogenetics, genotyping, and biobanking drive our mission. The emerging field of personalized medicine draws upon a person's genomic information to tailor treatments and prescription drug dosing to optimize health outcomes. The Coriell Personalized Medicine Collaborative (CPMC) research study is seeking to understand the usefulness of genetic risk and pharmacogenomics in clinical decision-making and healthcare management. Coriell has a distinguished history in cell biology. We are building upon this expertise by playing an important role in induced pluripotent stem (iPS) cell research. These powerful cells, which can be made from skin cells or blood, are revolutionizing the way human disease is studied and how drugs are developed. The decline of neurons afflicted with Alzheimer's disease or pancreatic cells fighting diabetes can be studied in a Petri dish. By proving efficacy within the diseased environment prior to clinical trial, drugs can move through the pipeline quicker to reach patients sooner. In addition to pioneering cutting-edge research initiatives, Coriell offers custom research services including cell culture, cytogenetic analyses, and molecular biology to the scientific community. Furthermore, Coriell's Genotyping and Microarray Center is one of the nation's largest centers, with high-throughput DNA analysis systems from Illumina and Affymetrix. The Center is CLIA-certified in 48 states.

Proper citation: Coriell Institute for Medical Research (RRID:SCR_003043) Copy   

•   Source: SciCrunch Registry
  

http://bluebrain.epfl.ch/

A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain.

Proper citation: Blue Brain Project (RRID:SCR_002994) Copy   

•   Source: SciCrunch Registry
  

http://platform.visiome.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.

Proper citation: Visiome Platform (RRID:SCR_003049) Copy   

•   Source: SciCrunch Registry
  

http://www.xnat.org

Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data.

Proper citation: XNAT - The Extensible Neuroimaging Archive Toolkit (RRID:SCR_003048) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/dalilite/indexhtml

Tool that computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol. The Dali method optimizes a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure. SOAP Web services are also available.

Proper citation: DaliLite Pairwise comparison of protein structures (RRID:SCR_003047) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/prorata/

A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.

Proper citation: ProRata (RRID:SCR_002988) Copy   

•   Source: SciCrunch Registry
  

https://bioimagesuiteweb.github.io/webapp/index.html

Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

Proper citation: BioImage Suite (RRID:SCR_002986) Copy   

•   Source: SciCrunch Registry
  

http://www.bioperl.org

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BioPerl (RRID:SCR_002989) Copy   

•   Source: SciCrunch Registry
  

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

•   Source: SciCrunch Registry