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https://github.com/armintoepfer/haploclique
Software providing a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.
Proper citation: HaploClique (RRID:SCR_002353) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 08, 2014. Project proposing a "liquid" format for science papers that consists of a set of research objects, connected by links. The immediate targets are the scientific research communities including publishers that, in a liquid world, will need to develop novel services and business models. Results and additional reading material (case studies, surveys, and the like) will be made available. The project also is creating an open source development effort and a platform to manage liquid publications and their evaluation. Their current main effort is developing the Liquid Journal and Liquid Conference use cases.
Proper citation: Liquid Publications: Scientific Publications meet the Web (RRID:SCR_002471) Copy
http://mialab.mrn.org/software/eegift/index.html
Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.
Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy
http://brainproducts.com/productdetails.php?id=17
Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.
Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy
http://www.nitrc.org/projects/pare/
A brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified.
Proper citation: M3 (RRID:SCR_002475) Copy
http://fged.org/projects/miame/
Standard specification for the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.
Proper citation: MIAME (RRID:SCR_002349) Copy
A interactive and highly effective educational resource and review for training in neuroscience and cognitive science. Supported by the Canadian institute of neurosciences, mental health and addiction; and Canadian institutes of health research.
Proper citation: The Brain from Top to Bottom (RRID:SCR_002662) Copy
http://rtimage.sourceforge.net/
Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data.
Proper citation: RT Image (RRID:SCR_002535) Copy
An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts.
Proper citation: ROBEX (RRID:SCR_002534) Copy
http://www.bioconductor.org/packages/devel/bioc/html/MethylAid.html
Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Proper citation: MethylAid (RRID:SCR_002659) Copy
https://www.nitrc.org/projects/rex/
A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial.
Proper citation: REX (RRID:SCR_002532) Copy
An collaborative tool which allows users to edit LaTeX documents in their browser. Multiple users can simultaneously access and edit the same LaTeX document and see the changes in real time. The latest version is available online, and the built in chat helps communicate with others while editing.
Proper citation: ShareLaTeX (RRID:SCR_002652) Copy
An open-source, web-based platform and suite of software tools for for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes - and collaborations between scientists. It preserves associations between them, along with information about the people and organizations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology. SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users. Access to the RESTful API to access the data within SEEK is available.
Proper citation: SEEK (RRID:SCR_002651) Copy
Public university in Bari, Italy that offers a variety of degree programs including agricultural science, economics, education, and veterinary medicine.
Proper citation: University of Bari; Bari; Italy (RRID:SCR_002647) Copy
http://sccn.ucsd.edu/wiki/SIFT
A GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals (EEG, ECoG, MEG, etc), preferably after transforming signals into the source domain. The toolbox consists of four modules: (1) Data Preprocessing, (2) Model Fitting and Connectivity Estimation, (3) Statistical Analysis, (4) Visualization, with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling (AMVAR) algorithms, including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate (in the time-frequency domain) a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time, frequency and anatomical source location.
Proper citation: Source Information Flow Toolbox (RRID:SCR_002561) Copy
Public research university and polytechnic education center in Aveiro, Portugal. It offers undergraduate, graduate and post-graduate degree programs in applied mathematics, physics, chemistry, telecommunications, robotics, bioinformatics, sea sciences, materials, design, business administration and industrial engineering.
Proper citation: University of Aveiro; Aveiro; Portugal (RRID:SCR_002565) Copy
X-ALD database initiated July 1999 by Hugo W. Moser, M.D. and Stephan Kemp, Ph.D. The primary aims of the database are: to catalogue and facilitate the analysis of X-ALD mutations; to provide background information on X-ALD; to provide links to X-ALD patient organizations; and to help with contacting and finding (local) X-ALD health care professionals. The purpose of the X-linked adrenoleukodystrophy database is to provide general educational information about X-ALD.
Proper citation: X-linked Adrenoleukodystrophy Database (RRID:SCR_002548) Copy
The system is a web-based portal which allows vendors to review Federal Procurement Opportunities over 25,000. From the sites main navigation page, users can view opportunities and awards as well as view a variety of information and resources. FBO now contains Recovery and Reinvestment Act actions. Vendors / citizens may search, monitor, and retrieve opportunities. Government users may post, manage, and award opportunities when logged in using their password protected account.
Proper citation: FedBizOpps.gov: Federal Business Opportunities (RRID:SCR_002587) Copy
Simple, menu-driven software toolbox for SPM 5/8 for exploratory data analysis for functional or structural images (.img / .nii) provides the user with several options: # a histogram of all non-zero voxel values in a brain image; # a scatter plot, Q-Q plot, or Bland-Altman plots comparing two images; # a surface plot of all voxel values at a particular axial slice; # easy Region of Interst (ROI)-based extraction of voxel values. Note: the toolbox calls various SPM 5/8 functions. The Q-Q plot function requires the MATLAB stats toolbox.
Proper citation: vis: SPM Visualized Statistics toolbox (RRID:SCR_002619) Copy
The NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies. More than 80,000 chemicals are registered for use in the United States. Each year, an estimated 2,000 new ones are introduced for use in such everyday items as foods, personal care products, prescription drugs, household cleaners, and lawn care products. We do not know the effects of many of these chemicals on our health, yet we may be exposed to them while manufacturing, distributing, using, and disposing of them or when they become pollutants in our air, water, or soil. Relatively few chemicals are thought to pose a significant risk to human health. However, safeguarding public health depends on identifying both what the effects of these chemicals are and at what levels of exposure they may become hazardous to humansthat is, understanding their toxicology. The program was created as a cooperative effort to: 1. Coordinate toxicology testing programs within the federal government. 2. Strengthen the science base in toxicology. 3. Develop and validate improved testing methods. 4. Provide information about potentially toxic chemicals to health, regulatory, and research agencies, scientific and medical communities, and the public. The need for a program like the NTP arose because of increasing scientific, regulatory, and Congressional concerns about the human health effects of chemical agents in our environment. Many human diseases were thought to be directly or indirectly related to chemical exposures; therefore, it was thought that decreasing or eliminating human exposures to those chemicals would help prevent some human disease and disability. Testing Information The NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying the tools of modern toxicology and molecular biology. This involves conducting toxicological evaluations of substances of public health concern, developing and validating improved (sensitive, specific, rapid) testing methods, developing approaches and generating data to strengthen the science base for risk assessment, and communicating with all stakeholders. The NTP plays a critical role in providing needed scientific data, interpretations, and guidance concerning the appropriate uses of data to regulatory agencies and other groups involved with health-related research. Through its interactive relationship with regulatory agencies, the NTP plays an indirect, but important role in shaping public health policy. Study Data Searches The National Toxicology Program makes available data from more than 500 two-year, two species, toxicology and carcinogenesis studies collected by the NTP and its predecessor, the National Cancer Institute's Carcinogenesis Testing Program, are stored in a database at NIEHS. The NTP database also contains the results collected on approximately 300 toxicity studies from shorter duration tests and from genetic toxicity studies, which includes both in vitro and in vivo tests. In addition, test data from the immunotoxicity, developmental toxicity and reproductive toxicity studies are continually being added to this database. Partnerships Through relationships with regulatory agencies, the NTP has an indirect role in shaping public health policy. Federal and state government agencies rely on the scientific knowledge and its interpretation provided by the NTP to make credible decisions that protect public health and the environment. The NTP also plays a critical role in: 1. Fostering interagency collaborations in research and exposure assessment 2. Providing information to regulatory agencies about alternative methods for toxicity testing, interpretation 3. Exploring new technologies for evaluating how environmental agents cause disease NTP conferences and workshops provide an opportunity for researchers, regulatory, policy makers, and the public to examine issues together, exchange information, and reach agreement on future directions of toxicology and risk assessment. Postdoctoral Training Program Opportunities Applied Toxicology and Carcinogenesis Training Program Fellowship in Toxicological Pathology Fellowship in Laboratory Animal Medicine
Proper citation: National Toxicology Program: Department of Health and Human Services (RRID:SCR_002616) Copy
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