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MIAME / Minimum Information About a Microarray Experiment
Provides a standard for recording and reporting microarray-based gene expression data. MIAME is a standard that includes (i) the normalization strategy (spiking, housekeeping genes, total array, other approach), (ii) the normalization and quality control algorithms used, (iii) the identities and location of the array elements serving as controls, as well as their type, and (iv) hybridization extract preparation, detailing how the control samples are included in sample targets prior to hybridization.
Typeset
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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.
ProCon / PROteomics CONversion Tool
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.
SPARC / Scholarly Publishing and Academic Resources Coalition
Enables the open sharing of research outputs and educational materials. SPARC aims to democratize access to knowledge, accelerate discovery, and increase the return on our investment in research and education. It places a premium on collaboration and collective action, and works to advance this mission through the development and leadership of active coalitions. SPARC focuses on collaborating with other stakeholders to build on the opportunities created by the Internet, promoting changes to both infrastructure and culture needed to make open the default for research and education.
MINSEQE / Minimum Information about a high-throughput SEQuencing Experiment
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) the description of the biological system, samples, and the experimental variables, (2) the sequence read data for each assay, (3) the summary data for the set of assays, (4) general information about the experiment and sample-data relationships, and (5) essential experimental and data processing protocols.
FCS / Flow Cytometry Standard
Obsolete
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.
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MultiCellDS / MultiCellular Data Standard
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.
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