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50x faster: speeding up an SQL-based legacy system with few changes
conference contribution
posted on 2023-05-23, 10:19 authored by Shi, L, Lenneke JongLenneke Jong, Mueller, W, Algaa, ESABIO-RK (http://sabio.h-its.org/) is a database for reaction kinetic data. Its complex schema led to slow querying. The challenge described in this paper is how to improve the speed with as few as possible changes in the time tested SABIORK code. The dilemma of whether to rewrite a whole system or to best reuse the expertise embodied in existing code appears often in existing, grown academic bio software solutions. We describe our solution that uses the existing SQL database for consistent data storage, and uses inverted indexes for fast retrieval. We further outline how we migrated to a new interface and RESTful web services in order to improve SABIO-RK code reuse and standards compliance.
The work presented in this paper has been partly funded by the DFG project "Integrierte webbasierte Forschungsinfrastruktur zur Speicherung und Bereitstellung quantitativer zeitaufgeloester Daten im Laborkontext und fuer die Wissenschaftsffentlichkeit”.
The work presented in this paper has been partly funded by the DFG project "Integrierte webbasierte Forschungsinfrastruktur zur Speicherung und Bereitstellung quantitativer zeitaufgeloester Daten im Laborkontext und fuer die Wissenschaftsffentlichkeit”.
History
Publication title
Lecture Notes in Informatics: Informatik 2011Volume
P192Editors
H-U Heiss, P Pepper, H Schlingloff, J SchneiderPagination
1-11ISBN
978-3-88579-286-4Department/School
Institute for Marine and Antarctic StudiesPublisher
Society for Computer SciencePlace of publication
GermanyEvent title
Informatik 2011Event Venue
Berlin, GermanyDate of Event (Start Date)
2011-10-04Date of Event (End Date)
2011-10-07Rights statement
Copyright unknownRepository Status
- Restricted