Kunzmann, Patrick ; Hamacher, Kay (2018)
Biotite: a unifying open source computational biology framework in Python.
In: BMC bioinformatics, 19 (1)
Artikel, Bibliographie
Dies ist die neueste Version dieses Eintrags.
Kurzbeschreibung (Abstract)
BACKGROUND
As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the programs are made for a specific task, hence the user often needs to combine multiple programs in order to reach a goal. This can make the data processing unhandy, inflexible and even inefficient due to an overhead of read/write operations. Therefore, it is crucial to have a comprehensive, accessible and efficient computational biology framework in a scripting language to overcome these limitations.
RESULTS
We have developed the Python package Biotite: a general computational biology framework, that represents sequence and structure data based on NumPyndarrays. Furthermore the package contains seamless interfaces to biological databases and external software. The source code is freely accessible at https://github.com/biotite-dev/biotite .
CONCLUSIONS
Biotite is unifying in two ways: At first it bundles popular tasks in sequence analysis and structural bioinformatics in a consistently structured package. Secondly it adresses two groups of users: novice programmers get an easy access to Biotite due to its simplicity and the comprehensive documentation. On the other hand, advanced users can profit from its high performance and extensibility. They can implement their algorithms upon Biotite, so they can skip writing code for general functionality (like file parsers) and can focus on what their software makes unique.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2018 |
| Autor(en): | Kunzmann, Patrick ; Hamacher, Kay |
| Art des Eintrags: | Bibliographie |
| Titel: | Biotite: a unifying open source computational biology framework in Python. |
| Sprache: | Englisch |
| Publikationsjahr: | 1 Oktober 2018 |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | BMC bioinformatics |
| Jahrgang/Volume einer Zeitschrift: | 19 |
| (Heft-)Nummer: | 1 |
| Zugehörige Links: | |
| Kurzbeschreibung (Abstract): | BACKGROUND As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the programs are made for a specific task, hence the user often needs to combine multiple programs in order to reach a goal. This can make the data processing unhandy, inflexible and even inefficient due to an overhead of read/write operations. Therefore, it is crucial to have a comprehensive, accessible and efficient computational biology framework in a scripting language to overcome these limitations. RESULTS We have developed the Python package Biotite: a general computational biology framework, that represents sequence and structure data based on NumPyndarrays. Furthermore the package contains seamless interfaces to biological databases and external software. The source code is freely accessible at https://github.com/biotite-dev/biotite . CONCLUSIONS Biotite is unifying in two ways: At first it bundles popular tasks in sequence analysis and structural bioinformatics in a consistently structured package. Secondly it adresses two groups of users: novice programmers get an easy access to Biotite due to its simplicity and the comprehensive documentation. On the other hand, advanced users can profit from its high performance and extensibility. They can implement their algorithms upon Biotite, so they can skip writing code for general functionality (like file parsers) and can focus on what their software makes unique. |
| ID-Nummer: | pmid:30285630 |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Computational Biology and Simulation |
| Hinterlegungsdatum: | 09 Okt 2018 08:22 |
| Letzte Änderung: | 03 Jul 2024 02:30 |
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| Suche nach Titel in: | TUfind oder in Google |
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Biotite: a unifying open source computational biology framework in Python. (deposited 01 Mär 2022 13:26)
- Biotite: a unifying open source computational biology framework in Python. (deposited 09 Okt 2018 08:22) [Gegenwärtig angezeigt]
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