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SimTandem is a database search engine for identification of peptide sequences from LC/MS/MS data. The engine can be used as an external tool in OpenMS/TOPP. SQID Open source: SeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry. Tide (rewrite of Crux) Open source
Python. PyCharm – Cross-platform Python IDE with code inspections available for analyzing code on-the-fly in the editor and bulk analysis of the whole project. PyDev – Eclipse-based Python IDE with code analysis available on-the-fly in the editor or at save time. Pylint – Static code analyzer.
GOMA is an open-source, parallel, and scalable multiphysics software package for modeling and simulation of real-life physical processes, with a basis in computational fluid dynamics for problems with evolving geometry. A generic finite element library written in C++ with interfaces for Python, Matlab and Scilab.
v. t. e. In software engineering, profiling ("program profiling", "software profiling") is a form of dynamic program analysis that measures, for example, the space (memory) or time complexity of a program, the usage of particular instructions, or the frequency and duration of function calls. Most commonly, profiling information serves to aid ...
Search engine indexing is the collecting, parsing, and storing of data to facilitate fast and accurate information retrieval. Index design incorporates interdisciplinary concepts from linguistics, cognitive psychology, mathematics, informatics, and computer science. An alternate name for the process, in the context of search engines designed to ...
Website. lucene .apache .org. Apache Lucene is a free and open-source search engine software library, originally written in Java by Doug Cutting. It is supported by the Apache Software Foundation and is released under the Apache Software License. Lucene is widely used as a standard foundation for production search applications.
C, C++, Data Parallel C++ and Fortran. A collection of design and analysis tools - vectorization (SIMD) optimization, thread prototyping, automated roofline analysis, offload modeling and flow graph analysis. Freeware and Proprietary. Available as part of Intel oneAPI Base Toolkit . Linux Trace Toolkit (LTT) Linux.
Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster: Protein: Steinegger M, Mirdita M, Galiez C, Söding J: 2017 USEARCH Ultra-fast sequence analysis tool: Both: Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics.