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  1. Article ; Online: A mixed-paradigm component architecture for implementing web-based game servers

    Friese Stefan / Rother Kristian

    Open Computer Science, Vol 6, Iss 1, Pp 25-

    2016  Volume 32

    Abstract: Games are a well-suited testbed for the development and evaluation of concepts and tools in artificial intelligence (AI). In our paper we outline the architecture of a web-based game server that was developed to support the teaching of artificial ... ...

    Abstract Games are a well-suited testbed for the development and evaluation of concepts and tools in artificial intelligence (AI). In our paper we outline the architecture of a web-based game server that was developed to support the teaching of artificial intelligence at the university level as well as research in the domain of AI and rule-based language development. The server combines a Prolog-based declarative approach with Java-based server technologies. The architecture consists of multiple, strictly separated components. Declarative components comprise the gameindependent core engine as well as game-dependent logic and visualization descriptions. General operations (e.g. user management, load balancing, match maintenance etc.) and rendering of the visualization descriptions with actual GUI techniques are implemented imperatively. External interfaces are provided to integrate remote developers and learners to facilitate usage beyond the borders of a single university.
    Keywords component architecture ; artificial intelligence ; computer science education ; gaming ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 401
    Language English
    Publishing date 2016-04-01T00:00:00Z
    Publisher De Gruyter
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online ; Thesis: Efficient use of a protein structure annotation database

    Rother, Kristian

    application to packing analysis

    2007  

    Author's details von Kristian Rother
    Language English
    Size Online-Ressource
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Humboldt-Univ., Diss--Berlin, 2006
    Database Former special subject collection: coastal and deep sea fishing

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  3. Article ; Online: Automated modeling of RNA 3D structure.

    Rother, Kristian / Rother, Magdalena / Skiba, Pawel / Bujnicki, Janusz M

    Methods in molecular biology (Clifton, N.J.)

    2014  Volume 1097, Page(s) 395–415

    Abstract: This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many ... ...

    Abstract This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.
    MeSH term(s) Models, Molecular ; Nucleic Acid Conformation ; RNA/chemistry ; Software
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2014
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-62703-709-9_18
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book: Datenanalyse mit Python

    McKinney, Wes / Rother, Kristian / Tismer, Chrisitan

    [Auswertung von Daten mit Pandas, NumPy und IPython ; aktuell zu Python 3]

    2015  

    Author's details Wes McKinney. Dt. Übers. von Christian Tismer und Kristian Rother
    Language German
    Size VII, 467 S., Ill., graph. Darst., 230 mm x 176 mm
    Edition 1. Aufl.
    Publisher O'Reilly
    Publishing place Heidelberg
    Document type Book
    ISBN 3960090005 ; 9783960090007
    Database Former special subject collection: coastal and deep sea fishing

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  5. Book ; Online ; Thesis: Efficient use of a protein structure annotation database

    Rother, Kristian [Verfasser]

    application to packing analysis

    2007  

    Author's details von Kristian Rother
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  6. Article ; Online: CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.

    Puton, Tomasz / Kozlowski, Lukasz P / Rother, Kristian M / Bujnicki, Janusz M

    Nucleic acids research

    2014  Volume 42, Issue 8, Page(s) 5403–5406

    MeSH term(s) Benchmarking ; Nucleic Acid Conformation ; RNA/chemistry ; Sequence Analysis, RNA ; Software
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2014-03-18
    Publishing country England
    Document type Letter ; Published Erratum
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gku208
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  7. Book: Managing your biological data with Python

    Via, Allegra / Rother, Kristian / Tramontano, Anna

    (A Chapman & Hall book ; Chapman & Hall/CRC mathematical and computational biology series)

    2014  

    Author's details Allegra Via; Kristian Rother; Anna Tramontano
    Series title A Chapman & Hall book
    Chapman & Hall/CRC mathematical and computational biology series
    Keywords Biology/Data processing ; Python (Computer program language)
    Language English
    Size XXV, 544 S., Ill., graph. Darst.
    Publisher CRC Press/Chapman & Hall
    Publishing place Boca Raton, Fla. u.a.
    Document type Book
    ISBN 143988093X ; 9781439880937
    Database Former special subject collection: coastal and deep sea fishing

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  8. Book: Managing your biological data with Python

    Via, Allegra / Rother, Kristian / Tramontano, Anna

    (A Chapman & Hall book ; Chapman & Hall/CRC mathematical and computational biology series)

    2014  

    Author's details Allegra Via; Kristian Rother; Anna Tramontano
    Series title A Chapman & Hall book
    Chapman & Hall/CRC mathematical and computational biology series
    Keywords Biology/Data processing ; Python (Computer program language)
    Language English
    Size XXV, 544 S., Ill., graph. Darst.
    Publisher CRC Press/Chapman & Hall
    Publishing place Boca Raton, Fla. u.a.
    Document type Book
    ISBN 143988093X ; 9781439880937
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  9. Article ; Online: ModeRNA: a tool for comparative modeling of RNA 3D structure.

    Rother, Magdalena / Rother, Kristian / Puton, Tomasz / Bujnicki, Janusz M

    Nucleic acids research

    2011  Volume 39, Issue 10, Page(s) 4007–4022

    Abstract: RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for ... ...

    Abstract RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.
    MeSH term(s) Models, Molecular ; Nucleic Acid Conformation ; RNA/chemistry ; RNA, Transfer/chemistry ; Sequence Alignment ; Sequence Analysis, RNA ; Software
    Chemical Substances RNA (63231-63-0) ; RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2011-02-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkq1320
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    Zs.A 1067: Show issues Location:
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  10. Article ; Online: RNA tertiary structure prediction with ModeRNA.

    Rother, Magdalena / Rother, Kristian / Puton, Tomasz / Bujnicki, Janusz M

    Briefings in bioinformatics

    2011  Volume 12, Issue 6, Page(s) 601–613

    Abstract: Noncoding RNAs perform important roles in the cell. As their function is tightly connected with structure, and as experimental methods are time-consuming and expensive, the field of RNA structure prediction is developing rapidly. Here, we present a ... ...

    Abstract Noncoding RNAs perform important roles in the cell. As their function is tightly connected with structure, and as experimental methods are time-consuming and expensive, the field of RNA structure prediction is developing rapidly. Here, we present a detailed study on using the ModeRNA software. The tool uses the comparative modeling approach and can be applied when a structural template is available and an alignment of reasonable quality can be performed. We guide the reader through the entire process of modeling Escherichia coli tRNA(Thr) in a conformation corresponding to the complex with an aminoacyl-tRNA synthetase (aaRS). We describe the choice of a template structure, preparation of input files, and explore three possible modeling strategies. In the end, we evaluate the resulting models using six alternative benchmarks. The ModeRNA software can be freely downloaded from http://iimcb.genesilico.pl/moderna/ under the conditions of the General Public License. It runs under LINUX, Windows and Mac OS. It is also available as a server at http://iimcb.genesilico.pl/modernaserver/. The models and the script to reproduce the study from this article are available at http://www.genesilico.pl/moderna/examples/.
    MeSH term(s) Amino Acyl-tRNA Synthetases/chemistry ; Amino Acyl-tRNA Synthetases/metabolism ; Base Sequence ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; RNA/chemistry ; RNA, Transfer/chemistry ; Sequence Alignment ; Software
    Chemical Substances RNA (63231-63-0) ; RNA, Transfer (9014-25-9) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-)
    Language English
    Publishing date 2011-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbr050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6262: Show issues Location:
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