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http://umcd.humanconnectomeproject.org
Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.
Proper citation: USC Multimodal Connectivity Database (RRID:SCR_012809) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
http://ciliate.org/index.php/home/welcome
TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases
Proper citation: TGD (RRID:SCR_012803) Copy
http://www.ritsumei.ac.jp/~akitaoka/index-e.html
This portal describes Professor Kitaoka Akiyoshi''s research in the science of visual illusions. Working as an associate professor at the Ritsumeiken University, Department of Psychology, he is one of the few researchers in Japan to be actively researching in this field of study. Professor Kitaoka defines an illusion as a misperception of a real object, adding that defining what is real is a difficult task that depends on recognition and epistemology. An illusion is formed when the perceived characteristics of the object differ from the physical characteristics. Professor Kitaoka first started studying visual illusions when working at the Tokyo Metropolitan Institute for Neuroscience, before coming to RU. He currently researches geometrical, color, lightness, and motion illusions and visual completion, and has become a prominent expert in the field, publishing a wide range of articles on the subject as well as the popular books Trick Eyes, Trick Eyes 2, Trick Eyes Graphics, and the Handbook of the Science of Illusion. To create his illusions, Professor Kitaoka uses graphic design software such as CorelDRAW, Adobe Illustrator, and the drawing software included in Microsoft Word in addition to making use of programming languages like Borland Delphi (Pascal). All of the images set out to test hypotheses that serve to advance his study of illusions and their applications for other visual functions. The goal of his research is to test visual mechanisms through visual illusions.
Proper citation: Akiyoshis illusion pages (RRID:SCR_013187) Copy
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
Proper citation: KEGG (RRID:SCR_012773) Copy
http://sourceforge.net/projects/meanmachine/
This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz.
Proper citation: Mean Machine (RRID:SCR_013103) Copy
The incidence of Creutzfeldt-Jakob disease (CJD) is monitored in the UK by the National CJD Surveillance Unit (NCJDSU) based at the Western General Hospital in Edinburgh, Scotland. The Unit brings together a team of clinical neurologists, neuropathologists and scientists specialising in the investigation of this disease. This document is intended to summarise the research in progress at the NCJDSU and also provide some background information about CJD and other human spongiform encephalopathies. We have also provided some links to other resources and contrary points of view available on the Web.
Proper citation: NCJDSU (RRID:SCR_013183) Copy
http://sourceforge.net/projects/liversegm/
Software tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation.
Proper citation: LiverSegm (RRID:SCR_013108) Copy
A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.
Proper citation: Abcam (RRID:SCR_012931) Copy
http://www.medicalimagecomputing.com/downloads/ems.php
EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase.
Proper citation: Expectation-Maximization Segmentation (RRID:SCR_013228) Copy
http://www.nactem.ac.uk/software/acromine/
An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE.
Proper citation: AcroMine (RRID:SCR_013196) Copy
http://www1.wfubmc.edu/PhysPharm/graduate/
The pursuit of the Department of Physiology & Pharmacology at Wake Forest University School of Medicine is excellence in research and education. Graduate education and training includes quality introductory and advanced courses in physiology, pharmacology and neuroscience, as well as seminars and journal clubs in several major research areas. Laboratory rotations encourage the graduate student to explore various experimental approaches and provide a diverse training experience. The department and Medical Center are frequented by distinguished visitors from other universities who further enrich the stimulating academic environment. Departmental faculty are active in the medical education as well as in residency training programs in Neurology, Psychiatry, Urology, and Surgery.
Proper citation: Wake Forest University Pharmacology (RRID:SCR_013111) Copy
A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.
Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy
An Antibody supplier
Proper citation: B-Bridge International (RRID:SCR_013559) Copy
http://www-sequence.stanford.edu/group/candida/
The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects.
Proper citation: Sequencing of Candida Albicans (RRID:SCR_013437) Copy
http://www.thermofisher.com/us/en/home/brands/molecular-probes.html?icid=fr-probe-main
An Antibody supplier and subset of ThermoFisher Scientific which provides fluorescence reagents for various experiments and methods.
Proper citation: Molecular Probes (RRID:SCR_013318) Copy
http://ncmir.ucsd.edu/downloads/montage_rts2000.shtm
Software program for creating montages from multiphoton microscopy.
Proper citation: Montage RTS2000 (RRID:SCR_013439) Copy
An Antibody supplier
Proper citation: Aviva Systems Biology (RRID:SCR_013560) Copy
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