Consists of a single-entry point to all minimum information checklists from the Genomic Standards Consortium (GSC) and to the environmental packages. MIxS is a framework that includes the technology-specific checklists from the MIGS and MIMS standards, provides a way of introducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages relevant to any genome sequence of known origin.
Provides open-source packages implementing the MAGE Object Model (MAGE-OM) in several programming languages. MAGE-STK is a suite of software developed to facilitate adoption of MAGE. The toolkit aims to provide an intermediate object layer that can then be used to export data to MAGE-ML, to store data in a persistent data store such as a relational database, or as input to software-analysis tools.
Permits an intuitive writing and collaboration, with the rigor and power of LaTeX. Typeset is a writing and collaboration tool for research papers and thesis documents. This editor comes with in-built tools for research related actions, removing all unwanted complexity in the research writing process. It enables with powerful tools to easily perform actions like adding and citing references, creating scientific expressions, cross referencing tables/equations/figures.
A Java application for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. ProCon converts Sequest.out, ProteinScape® and ProteomeDiscoverer® identification results, and outputs semantically enriched annotation of data in mzIdentML data format. ProCon can assist in preparing data submission to public repositories as recommended in the paper publication guidelines of major proteomics journals.
Furnishes a LaTeX document class corresponding to a standard document format for SBML Level 3 package. SBMLPkgSpec contains a wide range of features such as: (i) define SBML package version and SBML validation rules; (ii) format the names of common SBML object classes and XML primitive data types (iii) create new package-specific definitions (iv) use customized commands for cross-referencing sections, tables and figures.
Facilitates the development of software for reading and writing flow cytometry data. The goal of the Flow Cytometry Standard (FCS) is to provide a uniform file format that allows files created by any type of acquisition hardware to be analyzed by any third party data analysis tool. The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Finally, it includes simplified support for international characters and improved support for storing compensation.
Allows creation of clinical decision aids. DECIDE facilitates supportive functions of a genetic counsellor through patient-centred education and enhanced decision-making. It enables users to work individually, as a couple or family, or with a relative or friend, allowing patients to make decisions in ways that they find most comfortable and supportive. This tool provides an opportunity to make a decision about pharmacogenomics incidental findings or carrier status for recessive diseases.
Defines community standards for data representation in proteomics. HUPO-SPI aims to simplify data comparison, exchange and verification. It offers a solution for representing and exchanging protein interaction information. This data standard focuses on mass spectrometry and protein-protein interactions. It was developed in parallel of the PSI MI format allowing the combination of data from different sources.
Provides a list of verified ciliary genes, which can be used as a reference dataset of cilia genes. SCGS facilitates determination of objective cut-off thresholds via receiver operator characteristic (ROC) curves. It was constructed by collecting 27 ciliary studies from Cildb, which holds a large collection of ciliary datasets. The database can be used to train and evaluate bioinformatics tools, and can be considered as a reference resource.
A community-developed standard to functionally describe cell phenotypes with contextual information from the microenvironment. MultiCellDS is a library of over 200 digital cell lines contained a hierarchical, standardized yet extensible representation of a biological cell line’s phenotype in one or more microenvironmental contexts. Ultimately, MultiCellDS aspires to promote data sharing in computational and experimental biology and medicine, particularly cancer.
Provides information about high-throughput nucleotide sequencing experiments. MINSEQE avoids ambiguous interpretation and facilitates reproducibility of the results of experiments. Its utilization permits users to improve integration of multiple experiments across different modalities. This guideline contains: (1) description of biological system, samples, and experimental variables, (2) sequence read data for each assay, (3) summary data for set of assays, (4) general information about experiment and sample-data relationships, and (5) essential experimental and data processing protocols.
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