Effectopedia is a collaborative research platform for AOP development, modelling and use.
The knowledge (qualitative and quantitative) is organized in nested layers with different level of details.
The most abstract layer of pathway representation is a visual diagram of the pathway structure in which each element has its own graphical primitive with customizable annotation. The pathway diagram is automatically generated based on the biological context of the elements. The next level of details is captured in custom build interfaces for the individual elements (chemicals, effects, links, test methods, in silico models, etc.) and provides uniform representation of structured summary information.
In this layer for example in vitro test method description can have general definition of the test protocol, method performance and limitations, and a list of tested chemicals represented with their dose response curves. Each element can refer to additional details which for this example can include detailed description of the test protocol and raw experimental data for the tested chemicals. Some details of the description can be hosted and maintained by third parties.
Special efforts are also made for characterizing the uncertainties from different sources: 1) accuracy, variability and reproducibility of the experimental results, 2) the interpretation of assay outputs with respect to the associated in-vivo effect, and 3) the confidence with which the causality of the linkages between effects can be established.
The overall goal of Effectopedia is to aggregate, in a single source, all information needed to allow the development of quantitative AOPs and their use in decision making context.
Besides different groups of users like scientists, regulators, risk assessors, members of academia, industry, Non-Governmental Organizations (NGOs), and the general public, the structured knowledge will be also available as free web (API) services allowing further use from third party systems.
Hristo Aladjov, PhD
ENV/EHS, OECD, Paris, France
Administrator
>> SEE THE PRESENTATION <<
Aladjov H., Effectopeda | Free science and engineering downloads at sourceforge.net, 2014-07-18 http://sourceforge.net/projects/effectopedia/?source=directory
Veith G., Aladjov H., Effectopedia the online encyclopaedia of Adverse Outcome Pathways, 2014-07-18, http://www.effectopedia.org/
Effectopedia is a collaborative research platform for AOP development, modelling and use.
The knowledge (qualitative and quantitative) is organized in nested layers with different level of details.
The most abstract layer of pathway representation is a visual diagram of the pathway structure in which each element has its own graphical primitive with customizable annotation. The pathway diagram is automatically generated based on the biological context of the elements. The next level of details is captured in custom build interfaces for the individual elements (chemicals, effects, links, test methods, in silico models, etc.) and provides uniform representation of structured summary information.
In this layer for example in vitro test method description can have general definition of the test protocol, method performance and limitations, and a list of tested chemicals represented with their dose response curves. Each element can refer to additional details which for this example can include detailed description of the test protocol and raw experimental data for the tested chemicals. Some details of the description can be hosted and maintained by third parties.
Special efforts are also made for characterizing the uncertainties from different sources: 1) accuracy, variability and reproducibility of the experimental results, 2) the interpretation of assay outputs with respect to the associated in-vivo effect, and 3) the confidence with which the causality of the linkages between effects can be established.
The overall goal of Effectopedia is to aggregate, in a single source, all information needed to allow the development of quantitative AOPs and their use in decision making context.
Besides different groups of users like scientists, regulators, risk assessors, members of academia, industry, Non-Governmental Organizations (NGOs), and the general public, the structured knowledge will be also available as free web (API) services allowing further use from third party systems.
Accomplished research software developer with an interdisciplinary doctorate in motor control and artificial intelligence. Strong background in mathematics, algorithm development and computer visualization. Over 15 years of experience with design and implementation of innovative modeling software.
Education
Post-doctoral Research Fellow
2003-2006
U.S. Environmental Protection Agency, Mid-Continental Ecology Division in Duluth, MN, USA
Doctorate of Philosophy
Center of Biomedical Engineering, Bulgarian Academy of Science, Sofia, Bulgaria
1999-2002
Ph.D. thesis: Generalized net models of self-training processes and their applications for motor control investigations.
Master of Computer Science
Technical University, Department of Computer Science, Sofia, Bulgaria
1993-1998
Specialty: Computer Engineering. Graduate thesis: Generalized Nets in Machine Learning
2nd Specialty: Multimedia technologies
1994-1997
Secondary Education Sofia High School of Mathematics
1990-1993
Programmer-operator
GRANTS & Awards
7th FWP (Seventh Framework Programme), co-investigator
European Commission
2011-2013
Models for Ageing and Technological Solutions for Improving and Enhancing the Quality of Life (MATSIQEL)
National Science Fund, co-investigator
Ministry of Education, Bulgarian National Science Fund
2011-2013
Insilico study of effects of bioactive compounds: applications to objects of priority for human health and environment (DТК02/58)
National Science Fund, project leader
Ministry of Education, Youth and Science of Bulgaria
Muscle Model Composed of Motor Units and Software for Simulation of their Control by Means of Hierarchical Genetic Algorithm (DMU-02-5)
2010-2013
National Science Fund, co-investigator
Ministry of Education, Youth and Science of Bulgaria
2010-2013
Modeling Processes with Fixed Development Rules (DM-02-29)
UM/EPA Cooperative Training Partnership, Research Associateship
U.S. Natural Resources Research Institute
2006-2008
Computer Modeling Approaches for Simulating Chemical Metabolism
National Research Council Research Associateship at EPA
National Research Council, U.S. National Academies of Sciences
2003-2006
Computer Modeling Approaches for Predicting Toxicological Outcomes
Experience
Consultant
2013-present
Organisation for Economic Co-operation and Development, Paris, France
Development of Effectopedia and co-leading the OECD, JRC, EPA AOP-KB project
Associate Professor
2010-present
Institute of Biophysics and Biomedical Engineering, Sofia, Bulgaria
Lead investigator and co-investigator on motor control and computational toxicology research projects
Research Assistant
2008-2010
Centre of Biomedical Engineering, Sofia, Bulgaria
Development of motor control models of human activity
Research Scholar
2006-2008
Natural Resources Research Institute, Duluth, MN, USA
Improvement and redesign of metabolism simulator applicability domain definition by introducing formal methods considering chemical categories, levels of biological organization, experimental conditions and species.
Post-doctoral Research Fellow
2003-2006
US-Environment Protection Agency, Duluth, MN, USA
Development of automated software tools that facilitate the design of mechanistically grounded QSAR models, applicable to untested chemicals on EPA inventories. In this process algorithms for strategic chemical selection, chemical categorization, probabilistic classification and affinity modeling were created.
Principal Programmer
2000-present
Lab of Mathematical Chemistry, Burgas Technological University, Burgas, Bulgaria
Software design and implementation in the area of computational chemistry and QSAR.
Assistant Professor
2000-2001
Technical University Sofia, Sofia, Bulgaria
Department of Computer Science. Seminars at discipline Petri Nets
Research Assistant
1998-2003
Centre of Biomedical Engineering, Sofia, Bulgaria
Development of motor control models of human motion.
System Administrator and Developer
1996-1997
Omnitel Ltd, Sofia, Bulgaria
Development of GPS tracking system for transportation trucks.
Lecturer
1996-1997
Union “Knowledge” , Sofia, Bulgaria
Prequalification computer literacy instructor for Microsoft office products