|
LabKey Server
LabKey Server is a software suite available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources. Specific scientific applications and workflows can be added on top of the basic platform and leverage a data processing pipeline. License LabKey licenses LabKey Server and its documentation for free under the Apache License. Languages and extensibility The base platform is written in Java. It can be extended through the addition of Java-based modules or simple, file-based modules written in HTML, XML and JavaScript. The platform can also be extended using LabKey Server's Java, JavaScript, R, Python, Perl and SAS client libraries. History LabKey Server, originally known as the Computational Proteomics Analysis System (CPAS), was developed at the Fred Hutchinson Cancer Research Center to manage high volumes of data ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
|
Cross-platform
In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software requires a separate build for each platform, but some can be directly run on any platform without special preparation, being written in an interpreted language or compiled to portable bytecode for which the interpreters or run-time packages are common or standard components of all supported platforms. For example, a cross-platform application may run on Microsoft Windows, Linux, and macOS. Cross-platform software may run on many platforms, or as few as two. Some frameworks for cross-platform development are Codename One, Kivy, Qt, Flutter, NativeScript, Xamarin, Phonegap, Ionic, and React Native. Platforms ''Platform'' can refer to the type of processor (CPU) or other hardware on which an operating system (OS) or applicatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
 |
Flow Cytometry
Flow cytometry (FC) is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles. In this process, a sample containing cells or particles is suspended in a fluid and injected into the flow cytometer instrument. The sample is focused to ideally flow one cell at a time through a laser beam, where the light scattered is characteristic to the cells and their components. Cells are often labeled with fluorescent markers so light is absorbed and then emitted in a band of wavelengths. Tens of thousands of cells can be quickly examined and the data gathered are processed by a computer. Flow cytometry is routinely used in basic research, clinical practice, and clinical trials. Uses for flow cytometry include: * Cell counting * Cell sorting * Determining cell characteristics and function * Detecting microorganisms * Biomarker detection * Protein engineering detection * Diagnosis of health disorders such as blood cancers * Measur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
FlowJo
FlowJo is a software package for analyzing flow cytometry data. Files produced by modern flow cytometers are written in the Flow Cytometry Standard format with an .fcs file extension. FlowJo will import and analyze cytometry data regardless of which flow cytometer is used to collect the data. Operation In FlowJo, samples are organized in a "Workspace" window, which presents a hierarchical view of all the samples and their analyses (gates and statistics). Viewing an entire experiment in a Workspace permits organizing and managing complex cytometry experiments and produces detailed graphical reports. FlowJo's ability to automate repetitive operations facilitates the production of statistics tables and graphical reports when the experiment involves many samples, parameters and/or operations. Within a workspace, samples can be grouped or sorted by various attributes such as the panel of antibodies with which they are stained, tissue type, or patient from whom they came. When an operat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
|
CaBIG
The cancer Biomedical Informatics Grid (caBIG) was a US government program to develop an open-source, open access information network called caGrid for secure data exchange on cancer research. The initiative was developed by the National Cancer Institute (part of the National Institutes of Health) and was maintained by the Center for Biomedical Informatics and Information Technology (CBIIT). In 2011 a report on caBIG raised significant questions about effectiveness and oversight, and its budget and scope were significantly trimmed. In May 2012, the National Cancer Informatics Program (NCIP) was created as caBIG's successor program. History The National Cancer Institute (NCI) of the United States funded the cancer Biomedical Informatics Grid (caBIG) initiative in spring 2004, headed by Kenneth Buetow. Its goal was to connect US biomedical cancer researchers using technology known as grid computing. The program, led by the Center for Bioinformatics and Information Technology (CBI ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
|
Mascot (software)
Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm. Mascot is freely available to use on the website of Matrix Science. A license is required for in-house use where more features can be incorporated. History means MOWSE was one of the first algorithms developed for protein identification using peptide mass fingerprinting. It was originally developed in 1993 as a collaboration between Darryl Pappin of the Imperial Cancer Research Fund (ICRF) and Alan Bleasby of the Science and Engineering Research Council (SERC). MOWSE stood apart from other protein identification algorithms in that it produced a probability-based score for identification. It was also the first to take into account the non-uniform distribution of peptide sizes, ca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
|
Trans-Proteomic Pipeline
The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra. Software Components Probability Assignment and Validation PeptideProphet performs statistical validation of peptide-spectra-matches (PSM) using the results of search engines by estimating a false discovery rate (FDR) on PSM level. The initial PeptideProphet used a fit of a Gaussian distribution for the correct identifications and a fit of a gamma distribution In probability theory and statistics, the gamma distribution is a two-parameter family of continuous probability distributions. The exponential distribution, Erlang distribution, and chi-square distribution are special cases of the gamma distri ... for the incorrect identification. A later modification of the program allowed the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
|
Mass Spectrometry Software
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. Proteomics software In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and ''de novo'' search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data. Database search algorithms De novo sequencing algorithms De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels ''et al.'' (1990). Homology searching algorithms MS/MS peptide quantification Other software See also * Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters. * List of protein ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
|
Longitudinal Studies
A longitudinal study (or longitudinal survey, or panel study) is a research design that involves repeated observations of the same variables (e.g., people) over short or long periods of time (i.e., uses longitudinal data). It is often a type of observational study, although it can also be structured as longitudinal randomized experiment. Longitudinal studies are often used in social-personality and clinical psychology, to study rapid fluctuations in behaviors, thoughts, and emotions from moment to moment or day to day; in developmental psychology, to study developmental trends across the life span; and in sociology, to study life events throughout lifetimes or generations; and in consumer research and political polling to study consumer trends. The reason for this is that, unlike cross-sectional studies, in which different individuals with the same characteristics are compared, longitudinal studies track the same people, and so the differences observed in those people are less li ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
|
 |
Observational Study
In fields such as epidemiology, social sciences, psychology and statistics, an observational study draws inferences from a sample to a population where the independent variable is not under the control of the researcher because of ethical concerns or logistical constraints. One common observational study is about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator. This is in contrast with experiments, such as randomized controlled trials, where each subject is randomly assigned to a treated group or a control group. Observational studies, for lacking an assignment mechanism, naturally present difficulties for inferential analysis. Motivation The independent variable may be beyond the control of the investigator for a variety of reasons: * A randomized experiment would violate ethical standards. Suppose one wanted to investigate the abortion – breast can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
 |
Neutralizing Antibody
A neutralizing antibody (NAb) is an antibody that defends a cell from a pathogen or infectious particle by neutralizing any effect it has biologically. Neutralization renders the particle no longer infectious or pathogenic. Neutralizing antibodies are part of the humoral response of the adaptive immune system against viruses, intracellular bacteria and microbial toxin. By binding specifically to surface structures ( antigen) on an infectious particle, neutralizing antibodies prevent the particle from interacting with its host cells it might infect and destroy. Mechanism In order to enter cells, pathogens, such as circulating viral particles or extracellular bacteria, use molecules on their surfaces to interact with the cell surface receptors of their target cell which allows them to enter the cell and start their replication cycle. Neutralizing antibodies can inhibit infectivity by binding to the pathogen and blocking the molecules needed for cell entry. This can be du ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
 |
ELISA
The enzyme-linked immunosorbent assay (ELISA) (, ) is a commonly used analytical biochemistry assay, first described by Eva Engvall and Peter Perlmann in 1971. The assay uses a solid-phase type of enzyme immunoassay (EIA) to detect the presence of a ligand (commonly a protein) in a liquid sample using antibodies directed against the protein to be measured. ELISA has been used as a diagnostic tool in medicine, plant pathology, and biotechnology, as well as a quality control check in various industries. In the most simple form of an ELISA, antigens from the sample to be tested are attached to a surface. Then, a matching antibody is applied over the surface so it can bind the antigen. This antibody is linked to an enzyme and then any unbound antibodies are removed. In the final step, a substance containing the enzyme's substrate is added. If there was binding, the subsequent reaction produces a detectable signal, most commonly a color change. Performing an ELISA involves at lea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |