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http://scitools.idtdna.com/analyzer/Applications/OligoAnalyzer/

Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration.

Proper citation: Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) Copy   

•   Source: SciCrunch Registry
  

https://bioinformatics.ca/jobs

Job postings available to Bioinformatics.ca members. To become a member please sign up for an account. DISCLAMER: OICR and the Canadian Bioinformatics Workshops are not affiliated with and have not investigated the companies listing jobs on this site. OICR is not making any representations with respect to the positions and is not acting as an agent for the companies listed.

Proper citation: Bioinformatics Jobs Board (RRID:SCR_001484) Copy   

•   Source: SciCrunch Registry
  

https://www.unafold.org/

Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.

Proper citation: UNAFold (RRID:SCR_001360) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/LPE.html

Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions.

Proper citation: LPE (RRID:SCR_001364) Copy   

•   Source: SciCrunch Registry
  

https://www.ara.com/mppd/

Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition.

Proper citation: Multiple-Path Particle Dosimetry Model (RRID:SCR_001486) Copy   

•   Source: SciCrunch Registry
  

http://globin.cse.psu.edu/

Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

Proper citation: Globin Gene Server (RRID:SCR_001480) Copy   

•   Source: SciCrunch Registry
  

https://repository.niddk.nih.gov/study/45

Study group and network for a 2008 longitudinal study for the etiology, diagnosis, treatment, and outcome of acute liver failure in infants, children, and adolescents. Data from patients include urine, bile, serum, liver tissue, cell lines derived from fibroblast culture, and DNA.

Proper citation: Pediatric Acute Liver Failure Study (RRID:SCR_001478) Copy   

•   Source: SciCrunch Registry
  

http://www.well.ox.ac.uk/happy/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Proper citation: Happy (RRID:SCR_001395) Copy   

•   Source: SciCrunch Registry
  

http://www.retinalmaps.com.au/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded.

Proper citation: Retinal Topography Maps Database (RRID:SCR_001399) Copy   

•   Source: SciCrunch Registry
  

http://www.utdallas.edu/~kilgard/lectures.htm

List of lectures, slides and videos concerning neuroscience and neurophysiology.

Proper citation: Online Neuroscience Lectures - Maintained by the Kilgard Lab (RRID:SCR_001397) Copy   

•   Source: SciCrunch Registry
  

https://www.mristudio.org/

An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration

Proper citation: MRI Studio (RRID:SCR_001398) Copy   

•   Source: SciCrunch Registry
  

http://bmsr.usc.edu/software/pneuma/

A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer.

Proper citation: PNEUMA (RRID:SCR_001391) Copy   

•   Source: SciCrunch Registry
  

https://cde.nlm.nih.gov/

A repository of Common Data Elements (CDE). The CDE is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. Forms in the Repository might be original, or might recreate the format of real-world data collection instruments or case report forms. NIH has endorsed collections of CDEs that meet established criteria. NIH-endorsed CDEs are designated with a gold ribbon. Users can Browse NIH-Endorsed CDEs, Browse All CDEs, or Browse Forms.

Proper citation: NIH Common Data Element Repository (RRID:SCR_001390) Copy   

•   Source: SciCrunch Registry
  

http://radiology.arizona.edu/CGRI/

Biomedical technology resource center that develops new gamma-ray imaging instruments and techniques that yield substantially improved spatial and temporal resolutions. The Center makes its imagers and expertise available to a wide community of biomedical and clinical researchers through collaborative and service-oriented interactions. The collaborative research applies these new imaging tools to basic research in functional genomics, proteomics, cancer, cardiovascular disease and cognitive neuroscience, and to clinical research in tumor detection and other selected topics. There are five core research projects: * Detector technology research and development * Reconstruction algorithms and system modeling * Data acquisition, signal processing, and system development * Image-quality assessment and system optimization * Techniques for molecular imaging

Proper citation: Center for Gamma Ray Imaging (RRID:SCR_001384) Copy   

•   Source: SciCrunch Registry
  

https://factory.euromov.eu/sml/index.php

Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).

Proper citation: Semantic Measures Library (RRID:SCR_001383) Copy   

•   Source: SciCrunch Registry
  

https://codr.c-path.org/

A repository of de-identified control arm data of patients from clinical studies of Alzheimer's disease and Mild Cognitive Impairment. It provides the ability to analyze the data online with the R statistical analysis program, create and download standard reports, run complex queries, or download data to a desktop for further analysis. Additional data will be added to the database over time. Critical Path Institute consortia members and qualified researchers may upload and work on scientific data relevant to biomarkers of drug toxicity, neurodegenerative diseases, and patient-reported outcomes.

Proper citation: CODR: C PATH On Line Data Repository (RRID:SCR_001388) Copy   

•   Source: SciCrunch Registry
  

http://c-path.org/programs/camd/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8, 2022. Consortium developing new technologies and methods to accelerate the development and review of medical products for neurodegenerative diseases. It is focused on accelerating drug development for patients with chronic neurodegenerative disease, namely, Alzheimer's disease (AD) and Parkinson's disease (PD), by advancing drug development tools for evaluating drug efficacy, conducting clinical trials, and streamlining the process of regulatory review. The consortium focuses on sharing precompetitive patient-level data from the control arms of legacy clinical trials, developing new tools to be submitted to the regulatory agencies, and developing consensus data standards. CAMD has the following areas of focus: (1) qualification of biomarkers, (2) development of common data standards, (3) creation of integrated databases for clinical trials data, and (4) development of quantitative model-based tools for drug development. Regulatory milestones include a qualification opinion with EMA for the use of low baseline hippocampal volume for patient enrichment in pre-dementia trials, and most recently, positive regulatory decisions from the FDA and EMA for the use of a clinical trial simulation tool to aid in trials for mild to moderate stages of AD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CAMD (RRID:SCR_001389) Copy   

•   Source: SciCrunch Registry
  

http://www.salk.edu/labs/slesinger/index.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This lab is investigating the molecular details of how potassium ion channels open and close (i.e. gating), the cellular regulation of potassium channels in nerve cells, and more recently, their role in drug addiction and mental disorders. There are currently two related areas of focus in the lab. One main area of research is investigating the G protein regulation of GIRK channels, utilizing structural, biochemical and electrophysiological strategies. The other area extends from the G protein regulation experiments to studies that examine the role of GIRK channels in the neural response to drugs of abuse, utilizing biochemical, electrophysiological and behavioral strategies.

Proper citation: Salk Institute for Biological Studies - Slesinger Lab (RRID:SCR_001850) Copy   

•   Source: SciCrunch Registry
  

http://www.farsight-toolkit.org/wiki/FARSIGHT_Toolkit

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.

Proper citation: Farsight Toolkit (RRID:SCR_001728) Copy   

•   Source: SciCrunch Registry
  

http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm

THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CCAT (RRID:SCR_001843) Copy   

•   Source: SciCrunch Registry