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This blog is a collective open blog for the community to post news, scientific developments and results, comments, opinions, insights, links and discussions related to computer-based predictive toxicology. (For new users: you will also be able to post here once the webmaster has added you to the user group.)

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OpenTox Association, OpenTox Euro 2015

Posted by Barry Hardy at Jul 23, 2015 08:57 AM |

Following up on the initial OpenTox project which was funded by the EU under FP7, OpenTox has developed as an open standards platform supporting application and infrastructure development in predictive toxicology and safety assessment. The OpenTox Association was founded 27 March this year as an international member-based non-profit association.


The purpose of the Association is to promote the community-based exchange and use of open knowledge, software, methods, tools, data, reference resources, and standards in the scientific activities of predictive toxicology, safety assessment and risk management, including the 3Rs goal of the Reduction, Refinement and Replacement of Animal Testing. Working groups have been formed which working virtually on an ongoing basis to elaborate further the open standards and integrating resources approach developed by the OpenTox community.


The OpenTox Euro 2015 meeting takes place 30 Sept - 2 Oct in Dublin, Ireland. The conference theme is Reproducible High Quality Safety Science on Complex Systems and will include conference sessions on Information Requirements & Standards, Characterisation of Systems, High Content Screening, Metabolism,  Modelling Cellular Perturbations & Responses, Linking Parameters & Evidence across Scales, Simulation, Systems Biology and Knowledge Integration Supporting Decision Making.


OpenTox Association Working group meetings will be held on the topics of Application Programming Interfaces, Adverse Outcome Pathways, Data and Metadata Standards and Resource Deployment. The meeting will also include a General Assembly of the Association in addition to hands-on modelling and analysis sessions, poster session and knowledge cafes.


To submit an abstract for the meeting:

(Deadlines: 31 July for speaker program, 31 August for posters)


Information and updates on the program will be posted at:


Barry Hardy

President, OpenTox Association

On behalf of the Organising Committee


More information on the OpenTox Association:

OpenTox USA 2015

Posted by Barry Hardy at Oct 03, 2014 10:02 PM |

I am pleased to announce the program for the OpenTox USA 2015 meeting which will take place 10-12 Feburary at Johns Hopkins, Baltimore.

The goal of the meeting is to discuss and develop important components for driving 21st century approaches to safety assessment forward. We assume that collaboration driven by an open global platform and open standards will be a key success factor. Integrating heterogenous evidence supported by a common knowledge framework and ecosystem of tools and partners will enable practical application, judgements and decisions including industrial application and regulatory acceptance.

The program will involve conference sessions and associated hands-on workshops, poster session and knowledge cafes.

The main themes of the meeting are:

Data Science, facilitated by Barry Hardy (Douglas Connect)

Adverse Outcome Pathways, facilitated by Stephen Edwards (US EPA)

Exposure Modelling, facilitated by Tim Pastoor (Syngenta)

Integrating Evidence and Analysis, facilitated by Thomas Hartung (Johns Hopkins)

Risk Assessment & Management Applications, facilitated by Grace Patlewicz (Du Pont)


We are open for submission of abstracts for consideration for the program.

Further information on the program can be found at


On behalf of the OpenTox Community and the Organising Committee.


best regards

Barry Hardy


Douglas Connect GmbH

Baermeggenweg 14

4314 Zeiningen



OpenTox USA 2013 Meeting

Posted by Barry Hardy at Aug 26, 2013 01:53 PM |

The OpenTox USA 2013 community meeting on innovative developments and applications in predictive toxicology will take place in RTP, North Carolina 29 - 30 October. The meeting is being organised as a collaboration between OpenTox and ToxBank.

The preliminary program is available at:

The meeting provides an opportunity for researchers to learn about best  practices and new applications in data management, modelling and analysis applied for predictive toxicology and risk assessment purposes.

Abstracts for the poster session are being accepted through 31 August.

On behalf of the OpenTox USA 2013 Organising Committee,
we look forward to seeing you in Raleigh-Durham.

Barry Hardy (Douglas Connect)
Scott Auerbach (NIEHS)
Rusty Thomas (Hamner Institutes)
Asish Mohapatra (Health Canada)

OpenTox USA 2013

Hamner Conference Center, North Carolina Biotechnology Center

29 - 30 October

Topics: data management, in silico modelling and application development, integrated data analysis, biokinetics, cheminformatics, bioinformatics, weight of evidence, risk assessment.

Abstract Submission:


OpenTox Euro 2013 meeting program

Posted by Barry Hardy at Aug 07, 2013 01:35 PM |

OpenTox Euro 2013 logoThe OpenTox Euro 2013 community meeting on innovative developments and
applications in predictive toxicology will take place in Mainz 30 Sept -
2 October. The meeting is being organised as a collaboration between OpenTox and ToxBank.

The preliminary program is available at:

The meeting provides an opportunity for researchers to learn about best
practices and new applications in data management, modelling and analysis.

Hands-on interactive workshops will provide attendees the opportunity to
work on analysis and modelling problems with a variety of software

Abstracts for the poster session are being accepted through 31 August.

On behalf of the OpenTox Euro 2013 Organising Committee,
we look forward to seeing you in Mainz

Barry Hardy (Douglas Connect) and Stefan Kramer (Johannes Gutenberg University of Mainz)

OpenTox Euro 2013

Johannes Gutenberg University of Mainz, Mainz, Germany

30 September - 2 October

Session Topics: Integrated Data Analysis, Open Data, Open Source, Open
Standards, Systems Biology and Toxicology, Visualisation and Analysis,
Innovative Developments

Organising Committee: Barry Hardy (Douglas Connect), Andreas Karwath,
Stefan Kramer (Johannes Gutenberg University of Mainz), Nina Jeliazkova
(Ideaconsult), Egon Willighagen (Maastricht University), and Juergen
Borlak (Hannover Medical School)

Abstract Submission:


OpenTox workshop activities, SETAC Africa, Buea

Posted by Barry Hardy at May 31, 2011 07:44 AM |

Page for notes and files used in our workshop activities here today

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OpenTox 2011 InterAction Meeting

Posted by Barry Hardy at Mar 19, 2011 09:26 AM |

The OpenTox 2011 InterAction Meeting will take place 9-12 August 2011 at the Technical University of Munich, Germany.

This meeting will discuss latest developments in predictive toxicology, including in silico and in vitro  modelling, applications, REACH-relevant models, risk assessment and regulatory and industry needs. A pre-conference workshop on new developments in OpenTox methods and applications will be held 9 August.

More information including registration, abstract submission, bursary award, and deadlines is available at

Some guidance on what is needed for predictive toxicology infrastructure

Posted by Barry Hardy at Mar 18, 2011 02:55 PM |

OpenTox Coordinator Barry Hardy summarises some results and recommendations from the pre-AXLR8 OpenTox workshop discussions, held 30 May 2010 in Potsdam, Germany.

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Initiation of EuroEcoTox network

Posted by Barry Hardy at Mar 14, 2011 09:44 AM |

A two year Coordinating Action titled “European Network for Alternative Testing Strategies in Ecotoxicology (EUROECOTOX) was launched last December 1st, 2010 addressing the goal of ENV.2010.3.3.1-1 Reduction of the use of animals in eco-toxicological safety testing.

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OpenTox Prototype Evaluation, Improve API and Interface Designs

Posted by Barry Hardy at Mar 08, 2011 08:45 PM |

In the OpenTox report on Prototype Evaluation, Improve API and Interface Designs  available at, two initial OpenTox prototype applications were evaluated: ToxPredict ( which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate ( which builds and validates a predictive toxicity model based on an input toxicology dataset. Templates were created for the recording of user feedback and beta testing results; initial testing provided useful guidance for subsequent development which is ongoing and will be subject to further testing as OpenTox evolves towards its final prototype applications in 2011.

            The OpenTox Application Programming Interface (API) published openly at has already found interest in the cheminformatics and bioinformatics communities. Currently, integrations into several different software packages are under development. We have received feedback and demand for new features from these collaborating developer communities.

A platform for continuous availability and performance monitoring of selected OpenTox web services has been designed and deployed. We discuss the rationale for such monitoring and provide an overview of the results obtained so far.

            Based on initial evaluation and discussion of the OpenTox API in 2009, the API 1.1 was developed and released in late 2009, and included a commitment to the semantic representation of all OpenTox resources. Experiences with the API 1.1 during prototyping has led to numerous modifications and improvements which have been included in version 1.2 released in late 2010.


OpenTox Prototype Demonstration Server

Posted by Barry Hardy at Mar 08, 2011 08:40 PM |

OpenTox provides an interoperable, standards-based framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications.

OpenTox includes services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The services are operated on a network of publicly accessible prototype demonstration servers that are distributed over multiple locations and organisations. Every provider responsible for service contributions has a server running that contributes to the distributed OpenTox system. In the OpenTox report Prototype Demonstration Server available at we take a closer look at three example server implementations to describe the whole distributed prototype system. The report also provides insight into the technical details, e.g., what programming languages and technologies have been used. It provides example usages of the distributed system, so that potential contributors to the system have a key overview guidance at their hands that will, in addition to further online information on the OpenTox web resources (, enable easy access to the system itself and make contributions easier. 

Two initial OpenTox applications were prototyped as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.

Taverna ( has been used to provide a user friendly workflow system to access and combine OpenTox web services. It provides a user interface which can be used to generate arbitrary workflows from combinations of single OpenTox web services. The web services are combined by importing single web services and connecting their inputs and outputs using a point-and-click user interface.

Continuing effort will be carried out by OpenTox developers to meet current academic and industry challenges regarding interoperability of software components and integration of data, algorithm and model services within the context of tested Use Cases. The experience we have gained during this work should help speed up the development process towards this direction.

Automated Validation Report Generation with OpenTox

Posted by Barry Hardy at Mar 08, 2011 08:35 PM |

OpenTox is supporting the development of reporting capabilities for the generation and presentation of results of alternative testing methods including validation and reporting results of relevance to REACH[1]. The OpenTox report generating component generates reports to present the results of predictions and (Quantitative) Structure Activity Relationship ((Q)SAR) model validations to the user in a structured reporting format. OpenTox reporting formats are guided by standards, templates such as (Q)SAR Model Reporting Format (QMRF) and the (Q)SAR Prediction Reporting Format (QPRF)[2], and OECD validation principles, which specify that to facilitate the consideration of acceptance of a (Q)SAR model for regulatory purposes, it needs to be associated with the OECD Guidelines for (Q)SAR Validation[3].

The OpenTox report on Automated Validation Report Generation available at describes and documents the initial progress which has been achieved within OpenTox with respect to the creation of automated reporting facilities for validated (Q)SAR models of predictive toxicology data. Within the OpenTox framework, we have defined an Application Programming Interface (API) for the (Q)SAR reporting web service as part of the OpenTox validation API ( We have established web services to automatically generate QMRF reports, which summarize key information on (Q)SAR-based predictive toxicology models, including the results of any validation studies, structured according to the OECD (Q)SAR validation principles. The user may subsequently edit the reports using a QMRF Editor. OpenTox services have also been developed for the generation of QPRF reports for validated toxicology predictions. A QPRF Editor for the manual annotation of automatically generated QPRF reports has been developed. Both editors are implemented as standalone applications that can also be started with a web browser. The actual creation of the reports uses a separate OpenTox web service running in the background.  

The initial OpenTox reporting web services support rapid generation of REACH relevant documents in the form of standardized reports for (Q)SAR-based predictive toxicology models and their predictions. The reporting web services allow for the downloading and uploading of reports which may be saved locally or online, enabling the collaborative editing and sharing of reports. The reporting services should allow all current and future OpenTox applications to easily create and access reports on validated predictive toxicology models, which with the addition of authorization and authentication can include the use of confidential resources.

OpenTox Tutorials

Posted by Barry Hardy at Mar 08, 2011 07:25 PM |

The OpenTox Tutorial report represents a collection of tutorial materials on several OpenTox topics including walk-throughs of the two end user prototype applications ToxPredict and ToxCreate, illustration of the use of validation and reporting services applied to predictive toxicology models, the application of OpenTox facilities in a drug discovery workflow, and detailed instructions on how to get a system set up to host an OpenTox data service.

The tutorial example on the prototype OpenTox application ToxPredict ( accepts chemical structures and names as input from the user and generates toxicity reports based on various pre-calibrated toxicity models and existing toxicity data.

In the ToxCreate ( tutorial, the user provides a dataset of chemical structures and target variable data. ToxCreate subsequently builds and validates a Quantitative Structure-Activity Relationship (QSAR) predictive toxicology model. The user receives a reporting on details of model results and model predictions which they may examine, and including using the model for new predictions.

In the in vitro data model building tutorial, a predictive model is built based on in vitro data using OpenTox web services. Several models can be built and inspected based on application to the US EPA ToxCast dataset.

The tutorial on web validation and reporting web services, which are also behind the end user applications ToxPredict and ToxCreate, shows how cURL calls can be used to validate a predictive model or an algorithm. A number of different validation methods are used, including K-fold split, training-test-split and bootstrapping. Furthermore, QMRF reports are generated and visualized using the QMRF Editor web start application.

The objective of the ISSMIC data analysis tutorial is to illustrate searching facilities and data visualization tools in the OpenTox framework, specifically in the context of in vivo micronucleus mutagenicity assays contained within ISSMIC, a curated database, containing critically-selected information on chemical compounds tested with the assay.

A tutorial example of a predictive toxicology application in drug discovery is provided using the data on anti-malarial compounds made available at the ChEMBL Neglected Tropical Disease (NTD) archive ( The anti-malarial compounds are prioritized based on a strongly conservative model for predicting oral toxicity. Experimentally-determined cytotoxicities against human cells of the compounds predicted to be safe are further examined, and their mutagenicities predicted. Sites of cytochrome P450 metabolism are predicted for selected compounds with no mutagenicity alerts, low human cytotoxicity, but high anti-malarial activity.

A tutorial is provided to guide the user through the setup of an OpenTox data service based on the download of the AMBIT software and its subsequent installation either on Windows or Linux.

The tutorial report is available for download at

All tutorials and their updates wiil made available online shortly under (to be opened 14 March 2011).


Bioclipse application download with OpenTox interoperability

Posted by Barry Hardy at Mar 08, 2011 07:15 PM |


A promising interoperation between Bioclipse and OpenTox was achieved in Autumn 2010 by Ola Spjuth (blogging at, Egon Willighagen, and OpenTox developers, and first demoed at the OpenTox-EBI industry forum workshop on ontology and interoperability at Hinxton (16, 17 November).  It is I think a good early practical example of the value of ontology and interoperability and the applications it enables linked with the nascent semantic toxicology web, and has much promise for further development in the months and years ahead.

You can download the Bioclipse application that interoperates with OpenTox and try it out yourself using one of the following downloads for PC, Mac or linux:

Slides from Rhodes OpenTox Workshop

Posted by Barry Hardy at Sep 29, 2010 11:52 AM |

I have made a copy of the slides used in the OpenTox presentation on 19 September at the EuroQSAR meeting in Rhodes available at:

Development and Use of Predictive Toxicology Applications
Barry Hardy, Christoph Helma, Nina Jeliazkova, Olga Tcheremenskaia, Stefan Kramer, Haralambos Sarimveis and Andreas Karwath


Knowledge Fair Table B - Drug Discovery Application

Posted by Roman Affentranger at Sep 13, 2010 09:55 PM |

An example of a predictive toxicology application in drug discovery is given using the data on antimalarial compounds made available at the ChEMBL Neglected Tropical Disease (NTD) archive ( The data was imported and made available via a specially installed OpenTox dataset service, to emulate a drug discovery exercise working in a setup separate from public dataset services. OpenTox model services are used for predicting toxicities.

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Knowledge Fair Table D - Query & Access Toxicity Data

Posted by Jeliazkov Vedrin at Sep 13, 2010 09:15 PM |

In this workshop you will query and access toxicity data, which has been compiled from various public sources, further curated and available online in OpenTox dataset services. More advanced techniques for querying and accessing toxicity data through OpenTox APIs would be demonstrated at Table F - Techie Table: Create an OpenTox App.

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Knowledge Fair Table G - Validate your QSAR Model and Create a Report for Developers

Posted by Andreas Karwath at Sep 14, 2010 01:45 PM |

Participants in this table will validate algorithms and generate QMRF reports using curl.

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Knowledge Fair Table A - Build a Predictive QSAR Model and Validate it

Posted by Sopasakis Pantelis at Sep 14, 2010 01:15 AM |

Participants in this table will build, validate and examine QSAR models with the ToxCreate application.

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Knowledge Fair Table F - Techie Table

Knowledge Fair Table F - Techie Table

Posted by Sopasakis Pantelis at Sep 14, 2010 01:15 AM |

A description of the discussions and activities that will take place on the "Techie Table" during the OpenTox workshop in Rhodes (19 Sept. 2010).

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Knowledge Fair Table C - Build a Model Based on In-Vitro Data

Posted by Maunz Andreas at Sep 13, 2010 04:15 PM |

Summary: In this workshop, you will build a predictive model based on in-vitro data using OpenTox web services using a Graphical User Interface (GUI) and via the command line. Several models can be built and inspected.

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