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Brunn: an open source laboratory information system for microplates with a graphical plate layout design process
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Wikberg group)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. (Cancer Pharmacology and Informatics/Rolf Larsson)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Wikberg group)ORCID iD: 0000-0002-8083-2864
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology. (Cancer Pharmacology and Informatics/Rolf Larsson)
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2011 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 12, no 1, 179Article in journal (Refereed) Published
Abstract [en]

Background:

Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open system for handling plate design, and validation and preparation of data.

Results:

A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves.

Conclusions:

Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC50 values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.

Place, publisher, year, edition, pages
2011. Vol. 12, no 1, 179
Keyword [en]
brunn, microtiter, bioclipse, screening, information system, lis, lims
National Category
Pharmacology and Toxicology
Research subject
Bioinformatics
Identifiers
URN: urn:nbn:se:uu:diva-153210DOI: 10.1186/1471-2105-12-179ISI: 000292027200001PubMedID: 21599898OAI: oai:DiVA.org:uu-153210DiVA: diva2:415605
Available from: 2011-05-09 Created: 2011-05-09 Last updated: 2015-07-22Bibliographically approved
In thesis
1. Ligand-based Methods for Data Management and Modelling
Open this publication in new window or tab >>Ligand-based Methods for Data Management and Modelling
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Drug discovery is a complicated and expensive process in the billion dollar range. One way of making the drug development process more efficient is better information handling, modelling and visualisation. The majority of todays drugs are small molecules, which interact with drug targets to cause an effect. Since the 1980s large amounts of compounds have been systematically tested by robots in so called high-throughput screening. Ligand-based drug discovery is based on modelling drug molecules. In the field known as Quantitative Structure–Activity Relationship (QSAR) molecules are described by molecular descriptors which are used for building mathematical models. Based on these models molecular properties can be predicted and using the molecular descriptors molecules can be compared for, e.g., similarity. Bioclipse is a workbench for the life sciences which provides ligand-based tools through a point and click interface. 

The aims of this thesis were to research, and develop new or improved ligand-based methods and open source software, and to work towards making these tools available for users through the Bioclipse workbench. To this end, a series of molecular signature studies was done and various Bioclipse plugins were developed.

An introduction to the field is provided in the thesis summary which is followed by five research papers. Paper I describes the Bioclipse 2 software and the Bioclipse scripting language. In Paper II the laboratory information system Brunn for supporting work with dose-response studies on microtiter plates is described. In Paper III the creation of a molecular fingerprint based on the molecular signature descriptor is presented and the new fingerprints are evaluated for target prediction and found to perform on par with industrial standard commercial molecular fingerprints. In Paper IV the effect of different parameter choices when using the signature fingerprint together with support vector machines (SVM) using the radial basis function (RBF) kernel is explored and reasonable default values are found. In Paper V the performance of SVM based QSAR using large datasets with the molecular signature descriptor is studied, and a QSAR model based on 1.2 million substances is created and made available from the Bioclipse workbench.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2015. 73 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, ISSN 1651-6192 ; 200
Keyword
QSAR, ligand-based drug discovery, bioclipse, information system, cheminformatics, bioinformatics
National Category
Pharmaceutical Sciences Bioinformatics and Systems Biology
Research subject
Pharmaceutical Pharmacology; Bioinformatics
Identifiers
urn:nbn:se:uu:diva-248964 (URN)978-91-554-9237-3 (ISBN)
Public defence
2015-06-05, B22 BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2015-05-12 Created: 2015-04-09 Last updated: 2015-07-07

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Alvarsson, JonathanAndersson, ClaesSpjuth, OlaLarsson, RolfWikberg, Jarl
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