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http://neuroade.christakou.org/

At neuroade, a Cognitive Neuroscience Laboratory, we study change in brain and behavior across multiple time-scales. Researchers in the lab combine a variety of methodologies to answer specific questions about typical and atypical behavior and development. We use functional magnetic resonance imaging (fMRI), peripheral psychophysiology (such as skin conductance responses), behavioral testing, genotyping analysis, and computational modeling. Most of our work takes place at the Centre for Integrative Neuroscience and Neurodynamics (CINN), and we all live in the Department of Psychology at the University of Reading. Our research is divided into several distinct yet highly interlinked themes, all converging in their application to understanding psychopathology -- summarised here in no particular order: * Decision-making and the Evaluation of Decision Outcomes * Dimensions of Impulsivity as a Foraging Strategy * Adolescent Development * Computational Modeling Probes of Individual Differences

Proper citation: neuroade (RRID:SCR_006758) Copy   

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http://diabetes.niddk.nih.gov/dm/pubs/america/

A compilation and assessment of epidemiologic, public health, and clinical data on diabetes and its complications in the United States. Published by the National Diabetes Data Group of the National Institute of Diabetes and Digestive and Kidney Diseases, the book contains 36 chapters organized in five areas: * the descriptive epidemiology of diabetes in the United States based on national surveys and community-based studies, including prevalence, incidence, sociodemographic and metabolic characteristics, risk factors for developing diabetes, and mortality * the myriad complications that affect patients with diabetes * characteristics of therapy and medical care for diabetes * economic aspects, including health insurance and health care costs * diabetes in special populations, including African Americans, Hispanics, Asian and Pacific Islanders, Native Americans, and pregnant women. Diabetes in America, 2nd Edition, has been designed to serve as a reliable scientific resource for assessing the scope and impact of diabetes and its complications, determining health policy and priorities in diabetes, and identifying areas of need in research. The intended audience includes health policy makers at the local and Federal levels who need a sound quantitative base of knowledge to use in decision making; clinicians who need to know the probability that their patients will develop diabetes and the prognosis of the disease for complications and premature mortality; persons with diabetes and their families who need sound information on which to make decisions about their life with diabetes; and the research community which needs to identify areas where important scientific knowledge is lacking.

Proper citation: Diabetes in America (RRID:SCR_006754) Copy   

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http://www.aids.gov/podcast/podcast-gallery/

Podcasts from AIDS.gov, featuring information from the Federal government about HIV/AIDS prevention, testing, research, treatment, and using new media in response to HIV/AIDS. Categories include: Basic HIV information, New Media, Federal Programs and Policies, HIV/AIDS Awareness Days, and Real Stories.

Proper citation: AIDS.gov Podcast (RRID:SCR_006750) Copy   

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http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html

Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EDASeq (RRID:SCR_006751) Copy   

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http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

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http://www.genomesunzipped.org/

A group blog providing expert, independent commentary on the personal genomics industry. The goal of the project is to provide genetic testing consumers with independent and informed analysis of developments in the field of genetics and the genetic testing industry. Members of Genomes Unzipped include active researchers in various fields of genetics, as well as specialists in the legal and public health issues surrounding new genomic technologies. Many of us have also been extensively involved in public communication about genetics. Members of the group have had their DNA tested with a variety of products. We have released all of these genetic data openly to the public, both as raw data and in a custom genome browser. As the project proceeds we plan to obtain more genetic tests ����?? up to and including whole genome sequencing ����?? and to continue to release these data to the world. The group is also performing analyses of our own raw genetic data to illustrate fundamental concepts in genetics, using software written both by group members and other collaborators; and we����??ll be releasing the code for that software in our new code repository. As the project expands, we����??ll be looking to add data from other volunteers to the project, as well as to collaborate with other ����??genome hackers����?? on the development of new tools for exploring genetic data.

Proper citation: Genomes Unzipped (RRID:SCR_006870) Copy   

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http://www.physionet.org/physiotools/

Growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of the research projects that contribute software to PhysioToolkit is the extraction of hidden information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. Contributions of software to PhysioToolkit are welcome, http://physionet.org/guidelines.shtml#software-contributions

Proper citation: PhysioToolkit (RRID:SCR_006868) Copy   

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http://www.molecularimaging.vcu.edu/

The Center for Molecular Imaging integrates molecular imaging and molecular medicine with systems biology approaches to understand disease complexity, promising to provide predictive, preventative and personalized medicine that will transform health care. The multi-modality molecular imaging program is composed of individual but overlapping research themes with specific projects under each theme. As all projects are underpinned by methodology development in the chemistry, biology, physics and bioengineering of imaging, there is always a strong overlap and cross feed in terms of methods and assays. The research themes include: * Biomarker pharmacodynamic imaging of metabolism, proliferation, cell death and vascular perfusion * Molecular genetic imaging in developing multi-modal reporter gene-based probes * Molecular imaging of angiogenesis and its relation to tumor hypoxia * Multi-modal nanoparticle probes for drug delivery and molecular imaging, including cell and immune-based therapies * Radiolabeled drug pharmacokinetics and studies of drug discovery and structural biology using molecular imaging strategies * Development of nanotechnology molecular imaging systems * Imaging proteomic mass spectrometry * Molecular imaging and molecular pathology diagnostic research The Center for Molecular Imaging fosters collaborative research, bringing together the advances being made in technology-driven research such as bioengineering, chemical genomics and nanotechnology with biomedical research groups studying cell and molecular biology and radiobiology, biologically targeted therapeutics, immuno-based mechanisms, and drug and biomarker discovery. The aim is to develop and validate multi-modality molecular imaging tools that will facilitate the advancement of translational medicine and clinical science research in oncology and neuroscience as well as other clinical research areas. The center is equipped with laboratories for radiochemistry, analytical chemistry, molecular biology, nanotechnology and animal imaging, as well as a dedicated facility for translational clinical imaging. Imaging technologies within the center include Positron Emission Tomography/Computed Tomography (preclinical and clinical), Single Photon Emission Computed Tomography, optical imaging, autoradiography and multi-modality nanotechnology imaging. Molecular probe developments underpin the biological and biomedical research conducted using the above modalities.

Proper citation: Virginia Commonwealth University Medical Center, Center for Molecular Imaging (RRID:SCR_006869) Copy   

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http://www.microbeworld.org/index.php?option=com_content&view=category&layout=blog&id=99&Itemid=259

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. This Week in Parasitism (TWiP) is a podcast about eukaryotic parasites hosted by Vincent Racaniello and Dick Despommier. Following in the path of their successful podcast ''This Week in Virology'' (TWiV), they strive for an informal yet informative conversation about parasites which is accessible to everyone, no matter what their science background. As science Professors at Columbia University, they have spent their entire academic careers directing research laboratories focused on parasites (Dick) and viruses (Vincent). Their enthusiasm for teaching inspired them to reach beyond the classroom with new media. TWiP is for everyone who wants to learn about parasites in a relaxing way. Music used on TWiP is composed and performed by Ronald Jenkees and used with permission.

Proper citation: TWiP - This Week in Parasitism (RRID:SCR_006788) Copy   

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http://dally.nimh.nih.gov/matoff/matoff.html

An interactive analysis program that searches neurophysiological data and plots the results. MatOFF was developed especially for dealing with the complexities common to behavioral neurophysiological experiments. It runs under Windows 2000 or XP and relies on MATLAB version R11.1 (or above) for all operations. MatOFF searches a data file to locate and plot epochs (trials) of special interest to the investigator. Appropriate input data files have time-stamped event codes, usually including neuron action potential firing events (spikes), and digitized analog data. The user specifies a list of event code numbers that uniquely identify a sequence of events. MatOFF uses this sequence to search the raw data file, select the epochs that meet the criteria, time-shift the trials to align them on a common event, order the epochs based on user-selected criteria, and plot the results based on a collection of page formatting specifications. MatOFF will also save extracted data and some statistics to disk. Features: * Powerful, interactive searching tools for locating relevant experimental events * Compatible with Cortex data acquisition program * Compatible with Plexon data acquisition system * Flexible, publication-quality graphical display and printing * Comprehensive scripting language * Supports learning and other dynamic behavior * Integrated interface to MATLAB functions * Automatic alignment of trial data and generation of histograms * Large variety of options for selecting and ordering trial data * Descriptive and non-parametric statistics * XY analog displays * Data export with flexible format control * Up to 72 plots per page * Display templates can be saved and reloaded * Free for public or private use * Adaptable to almost any data file format

Proper citation: MatOFF (RRID:SCR_006821) Copy   

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http://sourceforge.net/projects/bmdexpress/

Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.

Proper citation: BMDExpress (RRID:SCR_006823) Copy   

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http://www.peptideatlas.org

Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database.

Proper citation: PeptideAtlas (RRID:SCR_006783) Copy   

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http://sourceforge.net/projects/mubiomics/

A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier.

Proper citation: mubiomics (RRID:SCR_006785) Copy   

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http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) Copy   

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http://compbio.bccrc.ca/software/mutationseq/

A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.

Proper citation: mutationSeq (RRID:SCR_006815) Copy   

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http://www.uni-rostock.de/en/

Public university located in Rostock, Mecklenburg-Vorpommern, Germany. Founded in 1419.

Proper citation: University of Rostock; Mecklenburg-Vorpommern; Germany (RRID:SCR_006816) Copy   

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

A controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users'' communities

Proper citation: Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology (RRID:SCR_006776) Copy   

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

A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

Proper citation: RIPSeeker (RRID:SCR_006810) Copy   

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http://cebs.niehs.nih.gov

Repository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency.

Proper citation: Chemical Effects in Biological Systems (CEBS) (RRID:SCR_006778) Copy   

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http://purl.bioontology.org/ontology/WB-LS

A structured controlled vocabulary of the development of Caenorhabditis elegans.

Proper citation: C. elegans Development Vocabulary (RRID:SCR_006811) Copy   

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