Life Sciences Open Source
EPAM Life Sciences has extensive experience and expertise in developing organic chemistry software products for use in life science companies, research institutes, and universities. Before joining EPAM Systems in June 2014 and becoming EPAM Life Sciences, GGA Software Services developed internally a series of cheminformatics tools, and decided to make these tools available to the open-source community. We are continuing to undertake this open-source initiative through EPAM, and we look forward to improving the existing tools and to developing new tools for your use.
Life Sciences Open Source¶
- Cloud Pipeline Genomics analysis and Scientific computing in the Cloud of your choice
- Provides the ability to build & run the customized scripts and workflows that support genomics analysis, modeling & simulation, and machine learning activities that are required to accelerate drug discovery research.
- Wraps Cloud compute and storage resources into a single service, providing an easy and scalable approach to accomplish a wide range of scientific tasks.
- Supports three main Cloud platforms: Amazon, Azure, Google.
- Med3web Viewer and Editor High performance web tool for advanced visualization and manipulation of medical images: MRI, CT, etc.
- Med3web Viewer creates a 3D model of a body part based on the set of plane images. It provides a crucial means for performing visual analysis of a patient’s anatomy for diagnosis, preoperative planning, and surgical training.
- Unique rendering algorithms and GPU processing approach provide high performance, smooth interaction and ability to convenient working regardless location and time.
- Try the Med3web demo online.
- Miew – 3D Molecular Viewer High performance web tool for advanced visualization and manipulation of molecular structures
- Miew provides a full-featured set of tools for 3D visualization and editing of small molecules as well as large molecular complexes, including abilities to view, analyze, and modify the 3D structure of a molecule.
- Miew integrates as a component into your pages or functions as a standalone HTML5 web application. The latest versions of WebGL-enabled desktop and mobile browsers are supported.
- Try the Miew demo online.
- New Genome Browser Web at a speed and functionality of desktop
- Visualization of Alignments, Variations, Structural Variations
- Embedded Protein structure viewer
- Integration with ENSEMBL, UniPROT, etc. and internal databases
- Fast access to huge (500 Gb and more) data files and to cloud data (Amazon S3, Hadoop, etc.)
- Try the NGB demo: Analize genome online
- Bingo Chemistry search engine for Oracle, Microsoft SQL Server and PostgreSQL databases
- Bingo is a RDBMS data cartridge that provides the industry’s next-generation, fast, scalable, and efficient storage and searching solution for chemical information.
- Bingo seamlessly integrates the chemistry into Oracle, Microsoft SQL Server and PostgreSQL databases. Its extensible indexing is designed to enable scientists to store, index, and search chemical moieties alongside numbers and text within one underlying relational database server
- Ketcher Web-based molecule sketcher
- Ketcher is a web-based chemical structure editor.
- Ketcher 2.0 demo: Edit molecules online
- Indigo Toolkit Universal cheminformatics
toolkit and API
- Indigo is a universal organic chemistry toolkit. It contains first-class tools for end users, as well as a documented API for developers. Indigo it is completely free and open-source, while also available on a commercial basis.
- Indigo-based command-line utilities
- Number of freely available cheminformatics KNIME nodes
- Indigo-based Java GUI applications
- Indigo ELN Open-Source Chemistry Electronic Lab Notebook
- Indigo ELN allows scientists to prepare, plan,manage and access relevant information regarding research work. Application helps to analyze and share research information. Flexiable experiment template allows to support various experiment type. New components can be included in the application without the need to change the core code.
- Indigo ELN v 2.0 is the next version of EPAM open-source Indigo ELN based on a completely different technology stack than v.1.0 and providing a new interface, new features, at the same time retaining all the functionality previously implemented.
- Imago OCR Chemical optical recognition toolkit
- Imago OCR is a toolkit for 2D chemical structure image recognition. It contains a GUI program and a command-line utility, as well as a documented API for developers. Imago is completely free and open-source, while also available on a commercial basis.
- Imago OCR demo: Recognize molecule images online (use Ketcher Recognize button)
- Parso Parso Java library
- Parso is a lightweight Java library that is designed to read SAS7BDAT datasets. The Parso interfaces are analogous to those that belong to libraries designed to read table-storing files
- Despite its small size, the Parso library is the only full-featured open-source solution to process SAS7BDAT datasets
- EPAM Selenium Framework Test automation using Selenium WebDriver
- Selenium Framework is a Java library developed for test automation using Selenium WebDriver. It is based on Maven structure and integrates with the TestNG testing framework.
- Selenium Framework provides rapid test automation for Web applications and allows focusing on substantial test development instead of tiresome testware maintenance.