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http://www.mged.org/Workgroups/MAGE/mage-ml.html

A language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms.

Proper citation: MicroArray and Gene Expression Markup Language (RRID:SCR_003023) Copy   

•   Source: SciCrunch Registry

http://nmf.jax.org/protocols.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Neuroscience Mutagenesis Facility of the Jackson Laboratory (NMF) was established to produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The protocols are available. The impetus for the program resulted from the recognition that * the value of genomic data would remain limited unless more information about the functionality of its individual components became available, and * the task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e. N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. Protocols: * Genetics ** Production of Mice for a Genome-Wide ENU Mutagenesis Screen ** Production of Mice using Chemical Mutagenesis of Mouse ES Cells * Protocols ** Step by step procedures-- Mouse mutagenesis with ENU ** Step by step procedures-- ES Cell mutagenesis with EMS * Phenotyping: Overview * Protocols:(currently only screens marked * are in use) ** Acoustic startle response (ASR) ** Auditory brainstem response (ABR) ** CLAMSTM(former CCMS) ** Creatine kinase ** Developmental Screen * ** Eye and Vision * ** Gait Analysis ** Gustation ** Observation * ** Seizure threshold * ** Additional Background Information

Proper citation: JAX Neuroscience Mutagenesis Facility Protocols (RRID:SCR_003021) Copy   

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https://github.com/PacificBiosciences/R-pbh5

Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5.

Proper citation: R-pbh5 (RRID:SCR_003026) Copy   

•   Source: SciCrunch Registry

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

Software function that calculates the isotopic pattern (fine structures) for a given chemical formula.

Proper citation: Isopat (RRID:SCR_003025) Copy   

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http://bioconductor.org/packages/release/bioc/html/BRAIN.html

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

Proper citation: BRAIN (RRID:SCR_003018) Copy   

•   Source: SciCrunch Registry

http://www.dtp.nci.nih.gov

Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Developmental Therapeutics Program (RRID:SCR_003057) Copy   

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

All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.

Proper citation: SASqPCR (RRID:SCR_003056) Copy   

•   Source: SciCrunch Registry

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

R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Proper citation: SurvComp (RRID:SCR_003054) Copy   

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

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

Proper citation: Parametric Time Warping (RRID:SCR_003053) Copy   

•   Source: SciCrunch Registry

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

An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.

Proper citation: Gutentag (RRID:SCR_003051) Copy   

•   Source: SciCrunch Registry

http://bodb.usc.edu/bodb/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet.

Proper citation: Brain Operation Database (RRID:SCR_003050) Copy   

•   Source: SciCrunch Registry

http://briansimulator.org/

Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Proper citation: Brian Simulator (RRID:SCR_002998) Copy   

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http://developingmouse.brain-map.org/

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Proper citation: Allen Developing Mouse Brain Atlas (RRID:SCR_002990) Copy   

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https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/pacBioToCA

A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

Proper citation: PacBioToCA (RRID:SCR_003044) Copy   

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https://github.com/PacificBiosciences/R-pbutils

An R software package providing plotting and convenience functions.

Proper citation: R-pbutils (RRID:SCR_002995) Copy   

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http://bibiserv.techfak.uni-bielefeld.de/dialign/

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

Proper citation: DIALIGN (RRID:SCR_003041) Copy   

•   Source: SciCrunch Registry

http://www.dana-farber.org/

Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.

Proper citation: Dana-Farber Cancer Institute (RRID:SCR_003040) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/gwas/

Catalog of published genome-wide association studies. Genome-wide set of genetic variants in different individuals to see if any variant is associated with trait and disease. Database of genome-wide association study (GWAS) publications including only those attempting to assay single nucleotide polymorphisms (SNPs). Publications are organized from most to least recent date of publication. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). Works with HANCESTRO ancestry representation.

Proper citation: GWAS: Catalog of Published Genome-Wide Association Studies (RRID:SCR_012745) Copy   

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http://www.scienceexchange.com/facilities/lifetein

LifeTein LLC, located in South Plainfield, New Jersey, was founded for its global custom peptide synthesis services, antibody production services and chemical services. LifeTein offers a wide range of custom research services and a staff of scientists with the first-hand campus-core-facility experience necessary to understanding the role of peptide and protein services in large research projects. LifeTein is the only peptide synthesis manufacturer to have developed its own line of PeptideSyn platform for peptide synthesis and AdjuBooster for antibody production.

Proper citation: LifeTein (RRID:SCR_012626) Copy   

•   Source: SciCrunch Registry

http://www.brain.northwestern.edu/index.html

The Cognitive Neurology and Alzheimer's Disease Center (CNADC) is a multidisciplinary organization dedicated to conducting research to discover how the brain coordinates mental functions such as memory, language, attention, and emotion; transferring the benefits of this research to patients with brain diseases that impair cognitive function; and training researchers and clinicians who want to work in this field. The CNADC's mission is to investigate the neurological basis of cognitive function, to elucidate causes of dementia, and to ensure that the patients and their families are the beneficiaries of resultant discoveries. * Clinical Services: Neurobehavior and Memory Health Clinical Services * Annual Grant Opportunities: Annual Core Pilot Project Funding Opportunities * Research Areas & Faculty: Alzheimer's Disease / Primary Progressive Aphasia / Frontal Dementia, Brain Endowment (Brains are permanently stored, and requests for tissue for research purposes are submitted to Dr. Bigio for review by the Northwestern Alzheimer's Disease Center); Cognitive Brain Mapping Group, Volunteer For A Study * Fellowships: Neuropathology Fellowship, Behavioral Neurology & Neuropsychiatry Fellowship * Training Programs: Mechanisms of Aging and Dementia (M.A.D.) Training Program; Training Program in the Neuroscience of Human Cognition

Proper citation: Northwestern University Cognitive Neurology and Alzheimers Disease Center (RRID:SCR_012747) Copy   

•   Source: SciCrunch Registry