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http://www.bh4.org/BH4DatabasesBiodef.asp

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Approximately 2% of newborns with hyperphenylalaninaemia are deficient in tetrahydrobiopterin. Selective screening must be performed in all instances where hyperphenylalaninaemia is detected by neonatal screening. In the last 20 years, 308 patients with tetrahydrobiopterin deficiencies have been recognized as a result of screening carried out, worldwide, in Departments of Paediatrics. Of these 308 patients, 181 suffered from 6-pyruvoyltetrahydropterin synthase deficiency, 92 from dihydropteridine reductase deficiency, 13 from pterin-4a-carbinolamine dehydratase deficiency, 12 from GTP cyclohydrolase I deficiency, and 10 are still unclassified. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Preliminary evaluation reveals that the degree of hyperphenylalaninaemia can vary from normal to 2500 mumol/L. Analyses of pterins in urine and measurement of dihydropteridine reductase activity from Guthrie cards are absolutely essential tests for accurate diagnosis. There is a regional (demographic) variation in the frequency of tetrahydrobiopterin deficiencies indicating the highest incidence in Saudi Arabia, probably a consequence of the high consanguinity rate.

Proper citation: International Database of Tetrahydrobiopterin Deficiencies (RRID:SCR_008171) Copy   

•   Source: SciCrunch Registry

https://www.bioinfor.com/peaks-studio/

Software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post translational modifications and sequence variants (mutations), and peptide/protein de novo sequencing.

Proper citation: PEAKS Studio (RRID:SCR_022841) Copy   

•   Source: SciCrunch Registry

http://www.bioquest.org/esteem/esteem_details.php?product_id=248

Software to allow construction, analysis, and simulation of complex models in spreadsheet format.

Proper citation: PopTools (RRID:SCR_022840) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/

American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California.

Proper citation: Illumina (RRID:SCR_010233) Copy   

•   Source: SciCrunch Registry

http://treestoolbox.org/

Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.

Proper citation: TREES toolbox (RRID:SCR_010457) Copy   

•   Source: SciCrunch Registry

https://www.particle-metrix.de/en/products/zetaview-nanoparticle-tracking.html

Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH.

Proper citation: ZetaView Nanoparticle Tracking Analyzer (RRID:SCR_016647) Copy   

•   Source: SciCrunch Registry

http://romi.bu.edu/elisa/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.

Proper citation: Evolutionary Lineage Inferred from Structural Analysis (RRID:SCR_002343) Copy   

•   Source: SciCrunch Registry

http://panomics.pnnl.gov/

Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use.

Proper citation: Proteomics Research Center for Integrative Biology (RRID:SCR_001098) Copy   

•   Source: SciCrunch Registry

http://lab.rockefeller.edu/chait/

Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available.

Proper citation: National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reliability/

Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.

Proper citation: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/pubs/MitoCarta/

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

Proper citation: MitoCarta (RRID:SCR_018165) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/gsea/msigdb/index.jsp

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy   

•   Source: SciCrunch Registry

https://www.microscop.ru/uploads/Helios-NanoLab-600i-ds-web.pdf

Scanning Electron Microscope advanced DualBeam for ultra-high resolution imaging, analysis and fabrication at the nanoscale. Helios NanoLab 600i builds on the success of FEI’s winning DualBeam series offering advances in ion beam, electron beam, patterning and range of features to make milling, imaging, analysis and sample preparation down to nanoscale.

Proper citation: FEI Helios Nanolab 600i DualBeam (RRID:SCR_027033) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/A45727

Ion Torrent Genexus Integrated Sequencer is part of the Ion Torrent Genexus System. Instrument that can automate library construction, templating, and sequencing in single-instrument run.

Proper citation: Ion Torrent Genexus Integrated Sequencer (RRID:SCR_026449) Copy   

•   Source: SciCrunch Registry

http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.

Proper citation: miRanalyzer (RRID:SCR_000163) Copy   

•   Source: SciCrunch Registry

http://www.project-redcap.org/

Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.

Proper citation: REDCap (RRID:SCR_003445) Copy   

•   Source: SciCrunch Registry

http://perso.telecom-paristech.fr/~cardoso/guidesepsou.html

Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to consider an analysis into linear components that would be "as independent as possible" as in ICA, but would be "livin" in subspaces of dimension greater than 1. This could be called "MICA" for Multi-dimensional Independent Component Analysis.

Proper citation: Blind Source Separation and Independent Component Analysis (RRID:SCR_002812) Copy   

•   Source: SciCrunch Registry

http://www.mrc-cbu.cam.ac.uk/Imaging

Portal where neuroimaging studies are carried out using a Siemens 3T Tim Trio Magnetic Resonance Imaging (or MRI) scanner that is wholly dedicated to studies in Cognitive Neuroscience. From emotions and memories to language and learning, functional neuroimaging is being applied in many different areas of Cognitive Neuroscience. In many cases, this research relies upon support from healthy volunteers although neuroimaging studies are also being conducted in various clinical populations, including depression, anxiety, Parkinson's disease and Alzheimer's disease.

Proper citation: CBU Imaging Wiki (RRID:SCR_003014) Copy   

•   Source: SciCrunch Registry

http://www.github.com/kmuench/16p_resource

Software tool as a code to support figure generation for the manuscript by Roth, Muench et al. Used to perform analysis.

Proper citation: 16p_resource Code (RRID:SCR_016845) Copy   

•   Source: SciCrunch Registry