Tools   Select Another Resource Report Type

http://www.research.chop.edu/

Scientific organization dedicated to advancing pediatric medicine through translational research. Founded in 1922, it is currently one of the largest pediatric research programs in the United States.

Proper citation: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA (RRID:SCR_003416) Copy   

•   Source: SciCrunch Registry
  

http://fcon_1000.projects.nitrc.org/indi/pro/Berlin.html

Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file).

Proper citation: Neuro Bureau - Berlin Mind and Brain Sample (RRID:SCR_003537) Copy   

•   Source: SciCrunch Registry
  

http://mods.rna.albany.edu

The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings. The authors invite comments concerning new entries, errors or omissions and on the format presently used for electronic access to the database.

Proper citation: RNA Modification Database (RRID:SCR_003535) Copy   

•   Source: SciCrunch Registry
  

https://github.com/dbitton/LaSSO

An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.

Proper citation: LaSSO (RRID:SCR_003418) Copy   

•   Source: SciCrunch Registry
  

https://cnu.edu/

Public university in Newport News, Virginia. Academic programs at CNU encompass more than 80 areas of study, from biology to business administration and political science to performing arts.

Proper citation: Christopher Newport University; Virginia; USA (RRID:SCR_003539) Copy   

•   Source: SciCrunch Registry
  

http://phosphat.uni-hohenheim.de/

Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required).

Proper citation: PhosPhAt (RRID:SCR_003332) Copy   

•   Source: SciCrunch Registry
  

http://clinicalinformatics.stanford.edu/projects/cdw.html

Research and development project at Stanford University to create a standards-based informatics platform supporting clinical and translational research. STRIDE consists of three integrated components: a clinical data warehouse, based on the HL7 Reference Information Model (RIM), containing clinical information on over 1.6 million pediatric and adult patients cared for at Stanford University Medical Center since 1995; an application development framework for building research data management applications on the STRIDE platform and a biospecimen data management system. STRIDE's semantic model uses standardized terminologies, such as SNOMED, RxNorm, ICD and CPT, to represent important biomedical concepts and their relationships. STRIDE receives clinical data for research use via HL7 feeds from both SUMC hospitals: Lucile Packard Children's Hospital and Stanford Hospital and Clinics. This clinical data is used to support a wide variety of translational research services including: * Anonymized Patient Research Cohort Discovery * Electronic Chart Review for Research * IRB-Approved Clinical Data Extraction * Biospecimen Data Management * Multimedia Research * Data Management and Research Registries STRIDE is a highly secure environment utilizing encryption, fine-grained access control, robust auditing and detailed data segregation. Additionally, STRIDE has a robust access control framework with well-defined access granting authorities and access control groups. Consequently STRIDE meets or exceeds the requirements of the HIPAA Privacy and Security regulations. Privacy protection is further enhanced by requiring IRB approval for all research projects using STRIDE clinical data. From a technology and standards perspective, STRIDE is hosted on the Oracle 11g database platform. STRIDE application software provides access to the web services of a three-tier infrastructures using SSL encryption with strong authentication. These programs are cross-platform, self-updating thick-client applications that provides a rich user interface for data entry, retrieval and review as well as image manipulation and annotation. STRIDE makes extensive use of XML technologies for representation of structured meta data, distributed systems technologies using JSON for secure remote communication between client and server, and Swing graphical interface components providing a rich widget-set as well as advanced imaging and graphing capabilities. Users of the STRIDE Research Desktop Client can perform rapid data entry into structured fields, compose complex queries, and interact securely with clinical, research and imaging data.

Proper citation: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse (RRID:SCR_003453) Copy   

•   Source: SciCrunch Registry
  

http://www.metafor-project.org/doku.php

A free and open-source add-on for conducting meta-analyses with the statistical software environment R.

Proper citation: metaphor (RRID:SCR_003450) Copy   

•   Source: SciCrunch Registry
  

http://prosite.expasy.org/

Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.

Proper citation: PROSITE (RRID:SCR_003457) Copy   

•   Source: SciCrunch Registry
  

http://everestbiotech.com/

An Antibody supplier

Proper citation: Everest Biotech (RRID:SCR_003456) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.12/bioc/html/minfi.html

Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.

Proper citation: SWAN (RRID:SCR_003455) Copy   

•   Source: SciCrunch Registry
  

http://medschool.creighton.edu/medicine/departments/pharmacology/

The primary instructional mission of the Department is to provide professional students with an understanding of the pharmacological basis of therapeutics. In addition to instruction of students in the medical, dental, pharmacy and nursing programs at Creighton, faculty are actively involved in both teaching and research training of graduate students. Ten departmental faculty work with an energetic group of graduate students, postdoctoral fellows and research staff in a congenial and collaborative environment. Faculty in the Department of Pharmacology at Creighton University School of Medicine reflect the complex scope of modern pharmacological research as they apply methods of systems and cell physiology, neuroscience, biochemistry, and cellular and molecular biology to better understand drug action. Departmental faculty are engaged in diverse areas of research including, but not limited to, G protein-coupled receptor signal transduction, regulators of G-protein signaling, regulation of receptor gene expression, control of neurotransmitter release, ion channel modulation, molecular pharmacology of excitatory neurotransmission, and cardiovascular and CNS drug discovery. These studies provide insight into the mechanisms of drug action and the means by which drug action is translated into responses in the cardiovascular system, the nervous system, exocrine glands and cancer cells.

Proper citation: Creighton University Department of Pharmacology (RRID:SCR_003333) Copy   

•   Source: SciCrunch Registry
  

http://caintegrator-info.nci.nih.gov/rembrandt

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory.

Proper citation: Glioma Molecular Dignostic Initiatives (RRID:SCR_003329) Copy   

•   Source: SciCrunch Registry
  

https://github.com/distrep/DMLT

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A machine learning toolbox written in Matlab and C that provides a general interface to support the integration of new statistical machine learning methods by writing high level wrappers. It allows complex methods to be built from simple building blocks and makes the use of cross-validation and permutation testing as easy as writing one line of Matlab code. The code requires at least Matlab distribution 7.6.0.324 (R2008a).

Proper citation: Donders Machine Learning Toolbox (RRID:SCR_003561) Copy   

•   Source: SciCrunch Registry
  

https://github.com/automaticanalysis/automaticanalysis

Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.

Proper citation: Automatic Analysis (RRID:SCR_003560) Copy   

•   Source: SciCrunch Registry
  

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

Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

Proper citation: BMIQ (RRID:SCR_003446) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/FB-SP

The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

Proper citation: Fly Taxonomy (RRID:SCR_003317) Copy   

•   Source: SciCrunch Registry
  

http://toliaslab.org/code-and-algorithms/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Code and algorithms produced by the Andreas Tolias lab (Baylor College of Medicine, Department of Neuroscience) where the goal is to understand the rules by which networks of nerves cells in the neocortex orchestrate their activity to process information; to decipher the neural code.

Proper citation: BCM Department of Neuroscience Andreas Tolias Lab (RRID:SCR_003594) Copy   

•   Source: SciCrunch Registry
  

http://www.ioos.noaa.gov/

Organization to lead the integration of ocean, coastal, and Great Lakes observing capabilities, in collaboration with Federal and non-Federal partners, to maximize access to data and generation of information products, inform decision making, and promote economic, environmental, and social benefits to the nation and the world. This national-regional partnership is working to provide new tools and forecasts to improve safety, enhance the economy, and protect the environment. Integrated ocean information is available in near real time, as well as retrospectively. Easier and better access to this information is improving their ability to understand and predict coastal events - such as storms, wave heights, and sea level change. Such knowledge is needed for everything from retail to development planning. The Integrated Ocean Observing System (IOOS) program achieves its objectives by funding organizations through a competitive process.

Proper citation: Integrated Ocean Observing System (RRID:SCR_003598) Copy   

•   Source: SciCrunch Registry
  

http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

•   Source: SciCrunch Registry