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http://www.biochem.mpg.de/5111795/maxquant

A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics.

Proper citation: MaxQuant (RRID:SCR_014485) Copy   

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http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT

Proper citation: Vienna RNA (RRID:SCR_008550) Copy   

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http://opm.phar.umich.edu/

Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.

Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy   

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http://www.chlamycollection.org/

Central repository that receives, catalogs, preserves, and distributes wild type and mutant cultures of the green alga Chlamydomonas reinhardtii, as well as useful molecular reagents and kits for education and research.

Proper citation: Chlamydomonas Resource Center (RRID:SCR_014960) Copy   

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http://chip-atlas.org/

Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA.

Proper citation: ChIP-Atlas (RRID:SCR_015511) Copy   

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http://www.thegpm.org/tandem/

Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.

Proper citation: X!Tandem (RRID:SCR_015645) Copy   

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http://drugcentral.org/

Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action.

Proper citation: DrugCentral (RRID:SCR_015663) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

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http://biorxiv.org/

A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version.

Proper citation: bioRxiv (RRID:SCR_003933) Copy   

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http://www.gensat.org/

Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

Proper citation: Gene Expression Nervous System Atlas (RRID:SCR_002721) Copy   

•   Source: SciCrunch Registry

http://swift.cmbi.ru.nl/gv/dssp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.

Proper citation: Database of Secondary Structure Assignments (RRID:SCR_002725) Copy   

•   Source: SciCrunch Registry

http://www.brc.riken.jp/inf/en

RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad.

Proper citation: RIKEN BioResource Center (RRID:SCR_003250) Copy   

•   Source: SciCrunch Registry

http://www.biopieces.org

A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014).

Proper citation: Biopieces (RRID:SCR_005783) Copy   

•   Source: SciCrunch Registry

http://genapha.icapture.ubc.ca/PathTutorial/

Web application to investigate gene-gene interactions in genetic association studies designed to: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PATH (RRID:SCR_009042) Copy   

•   Source: SciCrunch Registry

http://www.framinghamheartstudy.org/

A longitudinal, epidemiologic study to identify the common risk factors or characteristics that contribute to cardiovascular disease by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms or suffered a heart attack or stroke. Since that time the FHS has studied three generations of participants resulting in biological specimens and data from nearly 15,000 participants. Since 1994, two groups from minority populations, including related individuals have been added to the FHS. FHS welcomes proposals from outside investigators for data and biospecimens. The researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have continued to return to the study every two years for a detailed medical history, physical examination, and laboratory tests, and in 1971, the Study enrolled a second generation - 5,124 of the original participants'''' adult children and their spouses - to participate in similar examinations. In 1994, the need to establish a new study reflecting a more diverse community of Framingham was recognized, and the first Omni cohort of the Framingham Heart Study was enrolled. In April 2002 the Study entered a new phase, the enrollment of a third generation of participants, the grandchildren of the Original Cohort. In 2003, a second group of Omni participants was enrolled. Over the years, careful monitoring of the Framingham Study population has led to the identification of major CVD risk factors, as well as valuable information on the effects of these factors such as blood pressure, blood triglyceride and cholesterol levels, age, gender, and psychosocial issues. Risk factors for other physiological conditions such as dementia have been and continue to be investigated. In addition, the relationships between physical traits and genetic patterns are being studied. FHS clinical and research data is stored in the dbGaP and NHLBI Repository repositories and may be accessed by application. Please check the following repositories before applying for data through FHS. Investigators seeking data that is not available through dbGaP or BioLINCC or seeking biological specimens may submit a proposal through the FHS web-based research application. The FHS data repository may be accessed through this FHS website, under the For Researchers link, then Description of Data, in order to determine if and how the desired data is stored. Proposals may involve the use of existing data, the collection of new data, either directly from participants or from previously collected samples, images, or other materials (e.g., medical records). The FHS Repository also has biological specimens available for genetic and non-genetic research proposals. Specimens include urine, blood and blood products, as well as DNA.

Proper citation: Framingham Heart Study (RRID:SCR_008963) Copy   

•   Source: SciCrunch Registry

http://zork.wustl.edu/niaaa/

A multi-site, multi-disciplinary undertaking with the overall goals of characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. The study is being coordinated by the SUNY Health Science Center at Brooklyn (HSCB) under the leadership of Henri Begleiter. The study was initially funded by the National Institute of Alcohol Abuse and Alcoholism (NIAAA) in 1989. Additional useful information at http://www.niaaa.nih.gov/ResearchInformation/ExtramuralResearch/SharedResources/projcoga.htm

Proper citation: Collaborative Study on the Genetics of Alcoholism (RRID:SCR_013395) Copy   

•   Source: SciCrunch Registry

http://hereditaryhearingloss.org/

Overview of the genetics of hereditary hearing impairment for researchers and clinicians. The site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. For syndromic hearing impairment, only a few of the most frequent forms are covered. An atlas of cochlea with genes listed can be accessed from this site.

Proper citation: Hereditary Hearing Loss Homepage (RRID:SCR_006469) Copy   

•   Source: SciCrunch Registry

http://www.pombase.org/

Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions.

Proper citation: PomBase (RRID:SCR_006586) Copy   

•   Source: SciCrunch Registry

http://www.lipidmaps.org/

Multi-institutional supported website and database that provides access to large number of globally used lipidomics resources. Internationally led the field of lipid curation, classification, and nomenclature since 2003. Produces new open-access databases, informatics tools and lipidomics-focused training activities will be generated and made publicly available for researchers studying lipids in health and disease.

Proper citation: LIPID Metabolites And Pathways Strategy (RRID:SCR_006579) Copy   

•   Source: SciCrunch Registry

http://www.cochrane.org/editorial-and-publishing-policy-resource/cochrane-central-register-controlled-trials-central

A bibliographic database that provides a highly concentrated source of reports of randomized controlled trials. Records contain the list of authors, the title of the article, the source, volume, issue, page numbers, and, in many cases, a summary of the article (abstract). They do not contain the full text of the article. Cochrane Groups maintain and update Specialized Registers, which are collections of controlled trials relevant to the groups. CENTRAL is comprised of these Specialized Registers, relevant records retrieved from MEDLINE and EMBASE, and records retrieved through handsearching (planned manual searching of a journal or conference proceedings to identify all reports of randomized controlled trials and controlled clinical trials). The Cochrane Collaboration contracts a technology company, Metaxis, to merge the records from the sources outlined above and provide a data feed to the publisher. New and changed data are delivered to the publisher on a monthly basis.

Proper citation: Cochrane Central Register of Controlled Trials (RRID:SCR_006576) Copy   

•   Source: SciCrunch Registry