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A modified version of the Brain Extraction Tool (BET) that can process rodent brains.

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• SciCrunch
• 14 years ago - by Anonymous

Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots.

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• RRID
• 3 years ago - by Anonymous

Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software

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• SciCrunch
• 14 years ago - by Anonymous

Software workflow for streamlined assembly and binning of metagenomes. Used for assembly and binning of metagenomes. Performs quality control, basic functional and taxonomic annotation of assembled contigs, using NCBI COG database.

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• RRID
• 3 years ago - submitted by Vinicius W Salazar

Data analysis service that predicts tyrosine sulfation sites in protein sequences.

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• SciCrunch
• 12 years ago - by Anonymous

Research software used for post-processing of functional MRI, diffusion MRI, spectroscopy, and perfusion MRI data. It is written in Interactive Data Language.

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• SciCrunch
• 11 years ago - by Anonymous

Institutional resource collaboratively run by Office of Research Operations and Department of Pathology and Laboratory Medicine that provides services in support of Dartmouth Research Communities and in alignment with Institutional Review Board approved protocols including Clinical Trials. Provides collection, processing, storage, and distribution of annotated human bio-specimens to clinicians and other investigators in support of clinical trials, industry sponsored projects, and scientific investigations.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.

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• SciCrunch
• 13 years ago - by Anonymous

A tool that measures surface to surface distance between two triangle meshes using user-specified uniform sampling. Thus, users can choose finer sampling level to calculate errors to gain more accuracy in theerror space, or sparser sampling to gain speed and get an approximate feeling of error distribution between boundaries. Besides its pleasant visualization using the VTK library, MeshValmet also provides useful histogram and statistical information based on the sample errors, such as mean and median distance, root mean square distance, mean square distance, mean absolute distance, Hausdorff distance, 95 percentile, 68 percentile, etc. MeshValmet is based on the work of Nicolas Aspert, etc.: MESH: Measuring Errors between Surfaces using the Hausdorff distance in the proceedings of the IEEE Int. Conf. on Multimedia and Expo 2002 (ICME), vol. I, pp. 705-708. The calculation of the Dice's Coefficient is calculated by Joshua Stough using the concept of a Riemannian sum.

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• SciCrunch
• 14 years ago - by Anonymous

Core facility for the University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Promotes research in obesity and nutrition on campus by coalescing team science ventures, fostering development of trainees that are well positioned for interdisciplinary collaboration, and leveraging resources from existing institutional programs to spawn interdisciplinary team science and translational outreach programs related to nutrition and obesity.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

A non-profit organization that facilitates the donation of tissues. It supports healthcare agencies, coroners, medical examiners and funeral professionals through donations and training, as well as partnering with organizations that utilize tissue in medical care and research.

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• SciCrunch
• 16 years ago - by Anonymous

Software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.

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• SciCrunch
• 17 years ago - by Anonymous

The code that runs the OpenSAFELY platform used for analysis of electronic health records data.

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• RRID
• 3 years ago - by Anonymous

The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been made utilizing the principles of open source a research method that promotes free and open access to the design and production of goods and knowledge. Its use was made well-known through the creation of the Linux computer operating system, in which professionals share knowledge to make corrections and fix problems. Open source is commonly used by millions of people today through the Wikipedia online free encyclopedia, a collection of public entries on established subjects that allows anyone to make additions or corrections. The National Institute of Mental Health launched The Human Brain Project in 1993 to develop and support the new science of neuro-informatics. From this initiative, it became obvious what needed to be done. That's why we created the Sarah Jane Brain Virtual Center of Excellence an ecosystem for professionals and families dealing with PABI around the world and a vehicle to help implement the PABI Plan by establishing a model system for PABI.

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• SciCrunch
• 15 years ago - by Anonymous

A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).

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• SciCrunch
• 17 years ago - by Anonymous

Offers instrumentation dedicated to characterizing biomolecular conformations and interactions, as well as equipment for isolation and purification of macromolecules for subsequent detailed biophysical analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE.

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• SciCrunch
• 14 years ago - by Anonymous

A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject.

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• SciCrunch
• 14 years ago - by Anonymous

Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values.

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• RRID
• 3 years ago - submitted by Nadine Tatto