Topic
Open platform
About: Open platform is a research topic. Over the lifetime, 2575 publications have been published within this topic receiving 43399 citations. The topic is also known as: open platforms.
Papers published on a yearly basis
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TL;DR: This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization of ENDscript 2 and ESPript 3 to handle a large number of data with reduced computation time.
Abstract: ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization. It takes advantage of the new version 3 of ESPript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. From a single PDB entry or file, ENDscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. Furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. All this information and more are now mapped on interactive 3D PyMOL representations. Thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune ENDscript to their needs. ENDscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool Web servers, with both 2D and 3D representations. ENDscript 2 and ESPript 3 are freely available at http://endscript.ibcp.fr and http://espript.ibcp.fr, respectively.
4,722 citations
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TL;DR: The pymatgen library as mentioned in this paper is an open-source Python library for materials analysis that provides a well-tested set of structure and thermodynamic analyses relevant to many applications, and an open platform for researchers to collaboratively develop sophisticated analyses of materials data obtained both from first principles calculations and experiments.
2,364 citations
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TL;DR: The ImageJ project is used as a case study of how open‐source software fosters its suites of software tools, making multitudes of image‐analysis technology easily accessible to the scientific community.
Abstract: Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem.
2,081 citations
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10 Jul 2001TL;DR: An application program interface (API) provides a set of functions for application developers who build Web applications on Microsoft Corporation's.NET™ platform as mentioned in this paper. But the API does not provide any control mechanism.
Abstract: An application program interface (API) provides a set of functions for application developers who build Web applications on Microsoft Corporation's .NET™ platform.
1,343 citations
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TL;DR: Responding to the Internet and open source systems, three traditional vendors of proprietary platforms experimented with hybrid strategies which attempted to combine the advantages of open source software while retaining control and differentiation.
788 citations