Beta Faculty Department of Information and Computing Sciences Scientific research methods Wienand Omta Peter de Waal October 24, 2014 Design Science Research • Motivation and definition • Approach • Example: Automated microscopy – Analyze – Design – Implement – Evaluate • Other terms Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 2 What is Design Science Design Science The Design Research approach is the analysis and the use of the performance of new designed artefacts, to understand, explain or improve aspects of IT Use: a change for the end-user e.g. the way of working Performance: a change in features/characteristics e.g. faster, better Artefacts: Interface, design method, a software package Measuring improvements and at the same time insight in way of working Applied in medical-, technical, information and computing sciences Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 3 Applied fields • Computer science • Information Science • Human Computer Interaction (HCI) • Information retrieval (IR) Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 4 Natural versus Design Natural sciences: Body of knowledge about phenomena in the world that describes and explains behaviour and interaction. Design sciences, or sciences of the artificial: Body of knowledge about artificial phenomena designed to meet certain goals See AIS-net pages on Design Research : http://desrist.org/design-research-in-information-systems/ Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 5 Design cyclus Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 6 Design approach Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 7 Design Research cycle Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 8 Example in automated microscopy Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 9 High Content Screening • • • • • • Image based readout, automated microscopy Automated image analysis Data at single cell level Multivariate data (multiple parameters) Complex phenotypes, unexpected phenotypes Insight into mechanism of action and black box problem drs. ing. Wienand Omta Approach: What is the problem? Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 11 Problem I DMSO (control) Drug 1 @ 0.5 x LD50 STAUROSPORINE (Apoptosis-inducer) Drug 2 @ 0.5 x LD50 SIRAMESINE (LCD-inducer) drs. ing. Wienand Omta Problem II drs. ing. Wienand Omta Approach step 1: Analyze Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 14 Analysis I Singh, Carpenter and Genovesio (2014) Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 15 Analysis II • • • • Finding novelty in the data Lack of knowledge in bioinformatics and statistics No appropriate tools available Not sufficient computational power available Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 16 Approach step 2: Design Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 17 KDD Framework Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 18 Analysis method Young et al. 2008 drs. ing. Wienand Omta Final work analysis workflow Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 20 Approach step 3: Implementation Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 21 Implementation • • • • • • Web based platform Non expert users Decision supportive Logic: R CRAN Storage MYSQL Interface: PHP + JQUERY • Bootstrap (mobile devices) • Parallel programming • Uses HPC (for large jobs) Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 22 Approach step 3: Evaluation Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 23 Evaluation Multi parameter approach Select relevant parameters Single parameter approach vs. Select a single parameter Apply factor analysis - Find relevant hits Ranking Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 24 Evaluation vs. Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 25 Evaluation Multi parameter approach Single parameter approach 45 minutes vs. 8 months 44 parameters vs. 1 parameter Cell level data 11.3 GB vs. Well level data 42.4 MB Clustered and ranked vs. Ranked Six main biological processes found vs. Two main biological processes found Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 26 Other terms I Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 27 Other terms II Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 28 Questions? Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 29 Acknowledgements Prof. dr. Sjaak Brinkkemper Scientific Research Methods 2014/2015 – Wienand Omta, Peter de Waal October 24, 2014 30
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