Research Topics
| Ola SpjuthSummaryAffiliation: Uppsala University Country: Sweden Publications
| Collaborators
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Detail Information
Publications
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years onNoel M O'Boyle
Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, CO, Cork, Ireland
J Cheminform 3:37. 2011..abstract:..- Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and BioclipseLars Carlsson
Safety Assessment, AstraZeneca Research and Development, 43183 Molndal, Sweden
BMC Bioinformatics 11:362. 2010..Predicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive... - XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web servicesJohannes Wagener
Max von Pettenkofer Institut, Ludwig Maximilians Universitat, Munich, Germany
BMC Bioinformatics 10:279. 2009..Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use... - Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centreOla Spjuth
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
Bioinformatics 27:1719-20. 2011..A set of plugins were also developed which make the services available from the Bioclipse workbench for life science. Services are available at http://www.hivdrc.org/services... - Towards interoperable and reproducible QSAR analyses: Exchange of datasetsOla Spjuth
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
J Cheminform 2:5. 2010..This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data... - Bioclipse 2: a scriptable integration platform for the life sciencesOla Spjuth
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
BMC Bioinformatics 10:397. 2009..Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks... - Bioclipse: an open source workbench for chemo- and bioinformaticsOla Spjuth
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
BMC Bioinformatics 8:59. 2007..No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework... - Integrated decision support for assessing chemical liabilitiesOla Spjuth
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
J Chem Inf Model 51:1840-7. 2011..Bioclipse and the decision support implementation are free, open source, and available from http://www.bioclipse.net/decision-support ... - The C1C2: a framework for simultaneous model selection and assessmentMartin Eklund
Department of Pharmaceutical Pharmacology, Uppsala University, Box 591, BMC, SE 751 24 Uppsala, Sweden
BMC Bioinformatics 9:360. 2008..The results obtained with the C1C2 were compared to those obtained by employing repeated K-fold cross-validation for choosing and assessing a model... - Proteochemometric modeling of HIV protease susceptibilityMaris Lapins
Department of Pharmaceutical Pharmacology, Uppsala University, SE 751 24, Sweden
BMC Bioinformatics 9:181. 2008..The descriptions were correlated to the susceptibility data of 828 unique HIV protease variants for seven protease inhibitors in current use; the data set comprised 4792 protease-inhibitor combinations... - Proteochemometric modeling of the susceptibility of mutated variants of the HIV-1 virus to reverse transcriptase inhibitorsMuhammad Junaid
Department of Pharmaceutical Pharmacology, Uppsala University, Uppsala, Sweden
PLoS ONE 5:e14353. 2010..Computational models that correlate HIV drug susceptibilities to the virus genotype and to drug molecular properties might facilitate selection of improved combination treatment regimens... - An eScience-Bayes strategy for analyzing omics dataMartin Eklund
Department of Pharmaceutical Biosciences, Uppsala University, PO Box 591, SE 751 24 Uppsala, Sweden
BMC Bioinformatics 11:282. 2010..Moreover, the integration of omics data with other data sources is difficult to shoehorn into classical statistical models. This has resulted in ad hoc approaches to address specific problems... - Linking the Resource Description Framework to cheminformatics and proteochemometricsEgon L Willighagen
Uppsala University, Department of Pharmaceutical Biosciences, Box 591, SE 751 24 Uppsala, Sweden
J Biomed Semantics 2:S6. 2011..The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows... - Brunn: an open source laboratory information system for microplates with a graphical plate layout design processJonathan Alvarsson
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
BMC Bioinformatics 12:179. 2011.... - Computational toxicology using the OpenTox application programming interface and BioclipseEgon L Willighagen
Department of Pharmaceutical Bioinformatics, Uppsala University, Uppsala, Sweden
BMC Res Notes 4:487. 2011..abstract:.. - The LCB Data WarehouseAdam Ameur
The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
Bioinformatics 22:1024-6. 2006..lcb.uu.se/index.phtml?i_login=test. User accounts are created upon request. Additional facilities including plug-ins, user documentation and a password protected data storage system are available from http://www.lcb.uu.se/lcbdw.php..