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A workflow consists of an orchestrated and repeatable pattern of activity, enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms.
Symyx Technologies, Inc. was a company that specialized in informatics and automation products. Symyx provided software solutions for scientific research, including Enterprise Laboratory Notebooks and products for combinatorial chemistry. The software part of the business became part of Accelrys, Inc. in 2010 and then in 2014 this company merged with Dassault Systèmes. Symyx also offered laboratory robotics systems for performing automated chemical research, which in 2010 was spun out as Freeslate, Inc.
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.
Cheminformatics refers to use of physical chemistry theory with computer and information science techniques—so called "in silico" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such in silico techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied.
Quantitative structure–activity relationship models are regression or classification models used in the chemical and biological sciences and engineering. Like other regression models, QSAR regression models relate a set of "predictor" variables (X) to the potency of the response variable (Y), while classification QSAR models relate the predictor variables to a categorical value of the response variable.
Enterprise content management (ECM) extends the concept of content management by adding a timeline for each content item and, possibly, enforcing processes for its creation, approval, and distribution. Systems using ECM generally provide a secure repository for managed items, analog or digital. They also include one methods for importing content to bring manage new items, and several presentation methods to make items available for use. Although ECM content may be protected by digital rights management (DRM), it is not required. ECM is distinguished from general content management by its cognizance of the processes and procedures of the enterprise for which it is created.
MDL Information Systems, Inc. was a provider of R&D informatics products for the life sciences and chemicals industries. The company was launched as a computer-aided drug design firm in January 1978 in Hayward, California. The company was acquired by Symyx Technologies, Inc. in 2007. Subsequently Accelrys merged with Symyx. The Accelrys name was retained for the combined company. In 2014 Accelrys was acquired by Dassault Systemes. The Accelrys business unit was renamed BIOVIA.
BIOVIA is a software company headquartered in the United States, with representation in Europe and Asia. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.
Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well as academic research groups. It is a private company that was founded in 1994; it is based in Montreal, Quebec, Canada. Its main product, Molecular Operating Environment (MOE), is written in a self-contained programming system, the Scientific Vector Language (SVL).
Materials Studio is software for simulating and modeling materials. It is developed and distributed by BIOVIA, a firm specializing in research software for computational chemistry, bioinformatics, cheminformatics, molecular dynamics simulation, and quantum mechanics.
VisTrails is a scientific workflow management system developed at the Scientific Computing and Imaging Institute at the University of Utah that provides support for data exploration and visualization. It is written in Python and employs Qt via PyQt bindings. The system is open source, released under the GPL v2 license. The pre-compiled versions for Windows, Mac OS X, and Linux come with an installer and several packages, including VTK, matplotlib, and ImageMagick. VisTrails also supports user-defined packages.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
Molecular Discovery Ltd is a software company working in the area of drug discovery.
Discovery Net is one of the earliest examples of a scientific workflow system allowing users to coordinate the execution of remote services based on Web service and Grid Services standards. The system was designed and implemented at Imperial College London as part of the Discovery Net pilot project funded by the UK e-Science Programme. Many of the concepts pioneered by Discovery Net have been later incorporated into a variety of other scientific workflow systems.
A scientific workflow system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or workflow, in a scientific application.
Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA.
Pipeline Pilot is a desktop software program sold by Dassault Systèmes for processing and analyzing data. Originally used in the natural sciences, the product's basic ETL and analytics capabilities have broadened over time. The product is now used for data science, ETL, reporting, prediction, and analytics in a number of sectors. The main feature of the program is the ability to design data workflows using a graphical user interface. It is an example of visual and dataflow programming and has use in a variety of settings, such as cheminformatics and QSAR, Next Generation Sequencing, image analysis, and text analytics. It is not an 'object oriented' programming language.
Data lineage includes the data origin, what happens to it, and where it moves over time. Data lineage gives visibility while greatly simplifying the ability to trace errors back to the root cause in a data analytics process.
The BioCompute Object (BCO) Project is a community-driven initiative to build a framework for standardizing and sharing computations and analyses generated from High-throughput sequencing. The project has since been standardized as IEEE 2791-2020, and the project files are maintained in an open source repository. The July 22nd, 2020 edition of the Federal Register announced that the FDA now supports the use of BioCompute in regulatory submissions, and the inclusion of the standard in the Data Standards Catalog for the submission of HTS data in NDAs, ANDAs, BLAs, and INDs to CBER, CDER, and CFSAN.
Originally started as a collaborative contract between the George Washington University and the Food and Drug Administration, the project has grown to include over 20 universities, biotechnology companies, public-private partnerships and pharmaceutical companies including Seven Bridges and Harvard Medical School. The BCO aims to ease the exchange of HTS workflows between various organizations, such as the FDA, pharmaceutical companies, contract research organizations, bioinformatic platform providers, and academic researchers. Due to the sensitive nature of regulatory filings, few direct references to material can be published. However, the project is currently funded to train FDA Reviewers and administrators to read and interpret BCOs, and currently has 4 publications either submitted or nearly submitted.
Linguamatics, headquartered in Cambridge, England, with offices in the United States and UK, is a provider of text mining systems through software licensing and services, primarily for pharmaceutical and healthcare applications. Founded in 2001, the company was purchased by IQVIA in January 2019.
References
- ↑ "SciTegic Company Overview". businessweek.com. Archived from the original on April 30, 2011. Retrieved 29 May 2014.
- ↑ Farr-Jones, Shauna (16 Apr 2001). "Emerging company profile - SciTegic Data Pipelining" (PDF). Biocentury - The Bernstein Report on BioBusiness. Retrieved 29 May 2014.
- ↑ Accelrys announces merger with SciTegic
- 1 2 Brown, Robert D.; Varma-O'Brien, Shika; Rogers, David (2006). "Data Pipelines and Virtual Screening: Automating the Process". QSAR Comb. Sci. Wiley-VCH. 25 (12): 1181–1191. doi:10.1002/qsar.200610089.
- ↑ Warr, Wendy A. (2012). "Scientific workflow systems: Pipeline Pilot and KNIME". Journal of Computer-Aided Molecular Design. 26 (7): 801–804. doi:10.1007/s10822-012-9577-7. ISSN 0920-654X. PMC 3414708 . PMID 22644661.
