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

A fold change ranks ordering statistics based software for detecting differentially expressed genes.

Proper citation: FCROS (RRID:SCR_006195) Copy   

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http://www.microbeworld.org/index.php?option=com_content&view=category&layout=blog&id=107&Itemid=275

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. This Week in Microbiology (TWiM) is a new podcast about unseen life on Earth hosted by Vincent Racaniello and friends. Following in the path of his successful shows ''This Week in Virology'' (TWiV) and ''This Week in Parasitism'' (TWiP), Racaniello and guests produce an informal yet informative conversation about microbes which is accessible to everyone, no matter what their science background. As a science Professor at Columbia University, Racaniello has spent his academic career directing a research laboratory focused on viruses. His enthusiasm for teaching inspired him to reach beyond the classroom using new media. TWiM is for everyone who wants to learn about the science of microbiology in a casual way. While there are no exams or pop quizzes, TWiM does encourage interaction with the audience via comments on specific episodes, via email and voicemail at 908-312-0760. Listeners can also use MicrobeWorld to suggest topics for the show by submitting articles or papers to the site and tagging them with TWiM. Each week Racaniello will view the tagged content and select items for discussion. Co-hosts on TWiM include Ronald Atlas, Jo Handelsman, Margaret McFall-Ngai, Stanley Maloy, Elio Schaechter, and Michael Schmidt. Music used on TWiM is composed and performed by Ronald Jenkees and used with permission.

Proper citation: TWiM - This Week in Microbiology (RRID:SCR_006098) Copy   

•   Source: SciCrunch Registry
  

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

An ontology for sequence annotations and how to preserve them with reference sequences.

Proper citation: Reference Sequence Annotation (RRID:SCR_006095) Copy   

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http://www.templeton.org/

The John Templeton Foundation serves as a philanthropic catalyst for discoveries relating to the Big Questions of human purpose and ultimate reality. We support research on subjects ranging from complexity, evolution, and infinity to creativity, forgiveness, love, and free will. We encourage civil, informed dialogue among scientists, philosophers, and theologians and between such experts and the public at large, for the purposes of definitional clarity and new insights. Our vision is derived from the late Sir John Templeton''s optimism about the possibility of acquiring new spiritual information and from his commitment to rigorous scientific research and related scholarship. The Foundation''s motto, How little we know, how eager to learn, exemplifies our support for open-minded inquiry and our hope for advancing human progress through breakthrough discoveries. Our Core Funding Areas cover the full range of the Foundation''s activities and grantmaking. Science and the Big Questions is the largest of these Core Funding Areas and is further divided into several subfields. The descriptions and illustrative grants attached to the Core Funding Areas are not meant to be exhaustive, but they should give potential applicants a general understanding of the sorts of activities that the Foundation does and does not fund. Core Funding Areas: * Science and the Big Questions ** Mathematical and Physical Sciences ** Life Sciences ** Human Sciences ** Philosophy and Theology ** Science in Dialogue * Character Development * Freedom and Free Enterprise * Exceptional Cognitive Talent and Genius * Genetics

Proper citation: John Templeton Foundation (RRID:SCR_006092) Copy   

•   Source: SciCrunch Registry
  

http://modencode.org/

A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets.

Proper citation: modENCODE (RRID:SCR_006206) Copy   

•   Source: SciCrunch Registry
  

http://sparkinsight.org

A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality.

Proper citation: Spark (RRID:SCR_006207) Copy   

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http://www.shuttleworthfoundation.org/

Shuttleworth Foundation is supporting exceptional people to change the world. We provide funding for dynamic leaders who are at the forefront of social change. We identify amazing people, give them a fellowship grant, and multiply the money they put into their projects by a factor of ten or more. We are looking for social innovators who are helping to change the world for the better and are looking for some support through an innovative social investment model.

Proper citation: Shuttleworth Foundation (RRID:SCR_005930) Copy   

•   Source: SciCrunch Registry
  

http://polbase.neb.com/

Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.

Proper citation: Polbase (RRID:SCR_006107) Copy   

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http://www.cmhd.ca/

Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges

Proper citation: CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.biol.uoa.gr/human_gpdb/

A publicly accessible, relational database of human G-Proteins and their interactions with human GPCRs and Effectors. Advanced data integration techniques make Human-gpDB very rich in context since all of the bioentities are linked to a rich variety of external data sources. High quality visualization methods make the networks more informative and the extraction of information easier. Human-gpDB is currently a very useful tool for drug targeting investigation. The sequences of G-Proteins and GPCRs are classified according to a hierarchy of different classes, families and sub-families, whereas the Effectors sequences are classified in families, subfamilies and types, based on extensive literature search. The classification of GPCRs follows the IUPHAR classification, while the Effectors classification is a unique feature and is based on their function. The database currently holds information about 713 human GPCRs, 36 human G-Proteins and 99 human Effectors. The collection of the information about the interactions between these molecules was done manually and the current status of Human-gpDB reveals information about 1663 connections between GPCRs and G-Proteins and 1618 connections between G-Proteins and Effectors.

Proper citation: Human-gpDB (RRID:SCR_006223) Copy   

•   Source: SciCrunch Registry
  

http://www.wmkeck.org/

The W. M. Keck Foundation was established in 1954 in Los Angeles by William Myron Keck, founder of The Superior Oil Company. Our Foundation is one of the nation''s largest philanthropic organizations, with assets of more than $1billion. Mr. Keck envisioned a philanthropic institution that would provide far-reaching benefits for humanity. By taking a bold, creative approach to grantmaking, he created a legacy that the Foundation proudly upholds today. In recent years, the Foundation has focused on Science and Engineering Research; Medical Research; Undergraduate Education; and Southern California. Each of our grant programs invests in people and programs that are making a difference in the quality of life, now and for the future. Supporting pioneering discoveries in science, engineering and medical research has been our mandate for a half-century. By funding the work of leading researchers, the establishment of unique laboratories and research centers, and the purchase of sophisticated instruments, we are laying the groundwork for breakthrough discoveries and new technologies that will save lives, provide innovative solutions to complex problems and add immeasurably to our understanding of life on Earth and our place in the universe. We believe that a high-quality, well-rounded college education is vital for tomorrow''s leaders. The Foundation''s undergraduate education program promotes inventive approaches to instruction and effective involvement of students in research at colleges across the nation. Our support of Southern California-based organizations enriching the lives of our region''s residents has expanded and deepened over the years. We place a special emphasis on children, youth and their families, with the goal of providing safe, healthy, supportive environments that prepare children to succeed in school and in life.

Proper citation: W. M. Keck Foundation (RRID:SCR_006103) Copy   

•   Source: SciCrunch Registry
  

http://riodb.ibase.aist.go.jp/brain/index.php?LANG=ENG

Atlas of magnetic resonance images and histological sections of a Japanese monkey brain, Rhesus monkey and human. The Brain Explorer allows for display, magnification, and comparison these images. Other formats include a collection of .jpg images, Quicktime VR (allow user to zoom in), and EmonV, a voxel viewer for MacOS X.

Proper citation: Brain Atlas Database of Japanese Monkey for WWW (RRID:SCR_006104) Copy   

•   Source: SciCrunch Registry
  

http://www.unc.edu/

The University of North Carolina at Chapel Hill, also known as UNC-Chapel Hill, Chapel Hill, North Carolina, or simply Carolina is a public research university in Chapel Hill, North Carolina. It is the flagship of the 17 campuses of the University of North Carolina system.

Proper citation: University of North Carolina at Chapel Hill; North Carolina; USA (RRID:SCR_006100) Copy   

•   Source: SciCrunch Registry
  

http://afni.nimh.nih.gov/afni/

Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.

Proper citation: Analysis of Functional NeuroImages (RRID:SCR_005927) Copy   

•   Source: SciCrunch Registry
  

https://www.braintest.org/brain_test/BrainTest

A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.

Proper citation: Brain Test (RRID:SCR_006212) Copy   

•   Source: SciCrunch Registry
  

https://phenome.jax.org/centers/QTLA

Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.

Proper citation: QTL Archive (RRID:SCR_006213) Copy   

•   Source: SciCrunch Registry
  

http://www.nottingham.ac.uk/

Public research university in Nottingham, United Kingdom. It was founded as University College Nottingham in 1881, and was granted a royal charter in 1948.

Proper citation: University of Nottingham; Nottingham; United Kingdom (RRID:SCR_006210) Copy   

•   Source: SciCrunch Registry
  

http://epigenomegateway.wustl.edu/

Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis.

Proper citation: WashU Epigenome Browser (RRID:SCR_006208) Copy   

•   Source: SciCrunch Registry
  

http://restraintsgrid.bmrb.wisc.edu/NRG/MRGridServlet

Original NMR (nuclear magnetic resonance) data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED) respectively as described in the references. There are 9,672,968 parsed constraints in 7159 entries. (Mar. 2013)

Proper citation: NMR Restraints Grid (RRID:SCR_006127) Copy   

•   Source: SciCrunch Registry
  

http://www.umd.be/BRCA1/

The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau.

Proper citation: UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) Copy   

•   Source: SciCrunch Registry