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Data Management for Processing Molecules

Please always quote using this URN: urn:nbn:de:0297-zib-8358
  • Molecular dynamics simulations of possible ligands for proteins yield large amounts of data in the form of trajectories which are further processed in order to find metastable conformations. These conformations can then be used for docking between ligand and protein. Around this core computation procedure lots of other data have to be managed. It should also be possible for external users not involved in program development to perform computations. As a paradigm for other fields where a similar constitution of program usage and data processing is found we present a software architecture for data generation, access and management. Requirements for this system include: Ease of use, graphical user interface, persistent storage of data concerning molecules, users, programs, program parameters, metadata, and results. A mere storage in the file system would render a quick overview of data more or less impossible. On the other hand, storing large amounts of binary data in a database doesn't yield any advantage concerning speed of access. Therefore, a hybrid approach combining file system and database is appropriate. The system should be easily extensible by inserting new applications which can be controlled and whose results can be collected and stored. The software system described here consists of different components, the presentation layer (graphical user interface), the business logic, the persistence layer (relational database plus file system), and an interface to the compute cluster (batch system for parallel processing). We will discuss the alternatives and take a closer look at the components.

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Metadaten
Author:Alexander Steidinger
Document Type:ZIB-Report
Tag:b; fingerprints; molecular comparison; molecular structure; relational database; software architecture; thin client; web interface; web server
MSC-Classification:68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area) / 68Nxx Software / 68N15 Programming languages
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area) / 68Pxx Theory of data / 68P05 Data structures
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area) / 68Pxx Theory of data / 68P10 Searching and sorting
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area) / 68Pxx Theory of data / 68P20 Information storage and retrieval
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area) / 68Uxx Computing methodologies and applications / 68U35 Information systems (hypertext navigation, interfaces, decision support, etc.) [See also 68M11]
CCS-Classification:E. Data / E.1 DATA STRUCTURES
D. Software / D.2 SOFTWARE ENGINEERING (K.6.3) / D.2.11 Software Architectures (NEW)
H. Information Systems / H.2 DATABASE MANAGEMENT (E.5) / H.2.4 Systems
H. Information Systems / H.3 INFORMATION STORAGE AND RETRIEVAL / H.3.2 Information Storage
H. Information Systems / H.5 INFORMATION INTERFACES AND PRESENTATION (e.g., HCI) (I.7) / H.5.2 User Interfaces (D.2.2, H.1.2, I.3.6)
Date of first Publication:2004/12/21
Series (Serial Number):ZIB-Report (05-01)
ZIB-Reportnumber:05-01
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