Public deliverables
- D2.1: Use requirements and specification of the ACGT internal clinical trials
- D2.6: Report on ObTiMA as a GCP conformant software application
- D3.5: Grid Interoperability report
- D4.5: Service based access to Oncosimulator - report
- D5.1: Consolidated requirements and specifications for data access
- D5.8: Investigation of providing support to users concerning the exploration of available data sets
- D5.9: Report concerning lessons learnt and synergies with external initiatives
- D6.1: Consolidated Requirement Analysis for Data Mining, Analysis and the Visualization Environment
- D6.6: Interoperability of ACGT knowledge discovery services with existing bioinformatics tools
- D6.7: Prototype and report of the final ACGT analysis environment
- D7.1: Consolidated Requirements on ontological approaches for integration of multi-level biomedical information
- D7.8: Introduction of a new CT in ACGT: A Case study
- D7.9: Formal procedures and protocols for the semantic integration of clinical trials in ACGT
- D8.1: Consolidated requirements (including information flows) of the in silico simulation models
- D8.4: Report on the clinical adaptation and validation procedure of the Oncosimulator and its integration into the ACGT architecture
- D9.5: Report on the Final ACGT Workflow Environment
- D9.6: Report on the Final specifica-tions of meta-data for the ACGT da-ta, tools, services and workflows
- D10.1: Production of informed-consent form in compliance with the clinical trials, post-genomic research and genetic data handling requirements
- D10.2: The ACGT ethical and legal requirements
- D10.6.2: First results of the empirical survey
- D11.4: Requirements and guidelines for developing secured ACGT services
- D12.7: The TOP trial for the final ACGT demonstration
- D13.1 :Evaluation criteria and verification procedures of the ACGT platform
- D14.7: The ACGT Educational Video Report
- D15.6: Final report and analysis of project dissemination activities
- D16.4: The ACGT Competition Report
D2.1: Use requirements and specification of the ACGT internal clinical trials
The present deliverable presents the rational of the project, in a more explicit and detailed manner, as well as its specific objectives. It elaborates the adopted requirements engineering methodology adopted by the project and shortly present details of the Clinical Studies designed for the evaluation of the results of the project.
Explicit scenarios, presenting both user-driven stories expressing user-needs, as they are documented by representative users, as well as technology-driven description of requirements of the system under design, representing indicative functionality of the system, as understood by experienced technological experts, have been developed and are described. The various future user groups and stakeholders of the project's results are presented and analyzed. Initial user requirements and functional requirements of the ACGT platform are elaborated. These requirements will be further elicited in the various WPs of the project, as foreseen in the DoW.
With the initial requirements of the project in mind, a large number of data sources, tools, standards and technology are available for the different aspects of the intended system and significant R&D results are available in a number of related scientific domains.
PART 2 of the deliverable provides a detailed state-of-the-art review in all of the scientific areas relevant to the project.
D2.6: Report on ObTiMA as a GCP conformant software application
The intention of this deliverable is to report on the GCP criteria to make ObTiMA GCP conformant and to build the basis for certification of ObTiMA to use in GCP conform Trials. Requirements for GCP conformant software applications and tools are explained and an overview of the functionalities of ObTiMA including the Trial Outline Builder (TOB) is given. The steps towards a GCP conformant ObTiMA are listed and described. The certification of ObTiMA is not part of ACGT. Only important documents are listed how to proceed in ongoing projects to fulfil these criteria.
D3.5: Grid Interoperability report
Deliverable presents the ideas concerning interoperability of different components of ACGT architecture in a context of integrating some tools or services with other testbeds or exploiting external infrastructures for computation or storage.
D4.5: Service based access to Oncosimulator - report
The present document provides a description of Oncosimulator Service implementation. It is the alternative way of accessing Oncosimulator code integrated into workflow environment of ACGT.
D5.1: Consolidated requirements and specifications for data access
This report comprises the first deliverable of WP5 of the ACGT project. A main goal of this work package is to provide seamless and interoperable data access to the distributed data sources that are relevant to each of the ACGT clinical trials by developing a set of compatible software modules and services based on web services. The main objective of this deliverable is to consolidate the user requirements defined in WP2 with respect to distributed data access. For this purpose we use the CAFCR architecting framework. This deliverable contains a chapter for each of the five CAFCR views: the Customer View, the Application View, the Functional View, the Conceptual View, and the Realization View.
Using this structure, we not only document the requirements for data access in more detail, but also make first steps towards a solution. This deliverable documents what has been done so far in WP5, and concludes by outlining what is next.
D5.8: Investigation of providing support to users concerning the exploration of available data sets - D5.9: Report concerning lessons learnt and synergies with external initiatives
In this deliverable we discuss the main ACGT results with respect to providing uniform access to relevant heterogeneous data sources and identify the main learning points that will drive our future work. The deliverable also describes state of the art solutions for enabling the users to explore the available datasets, a need identified as relevant in ACGT. Part of this deliverable, we also look at possible synergies with relevant external initiatives and summarize the results of the study concerning the use of ACGT outcomes to support a large and innovative research program of the Breast International Group, NeoBIG. Based on the requirements of the NeoBIG program we have evaluated the benefits and the issues related to the ACGT approach, the technical solutions and the expertise that we could bring to support NeoBIG and the new research work that is required. The future research work with focus on the NeoBIG program will be part of the INTEGRATE project which is briefly described at the end of this document.
D6.1: Consolidated Requirement Analysis for Data Mining, Analysis and the Visualization Environment
The present document provides an overview of the contributions of individual partners in ACGT WP6. The contributions are as follows: SIB provides datasets based on actual clinical-trial for testing, FhG addresses data mining tools and use of R in a grid environment, LundU addresses database developments and analysis tools based on pathway information, Biovista proposes a literature-based analysis tool, INRIA develops new clustering algorithms, UPM addresses the use of ontologies in the clinical data analysis, and UvA proposes a framework for interactive visualization.
D6.6: Interoperability of ACGT knowledge discovery services with existing bioinformatics tools - D6.7: Prototype and report of the final ACGT analysis environment
The purpose of this deliverable is to describe the final ACGT data analysis environment. In a nutshell, data analysis in the ACGT system is performed by accessing the data to analyse following the ACGT multi-level data integration approach (cf. Deliverable D7.10) and orchestrating a pipeline of data analysis services in the form of an analysis workflow in the ACGT Workflow Environment (cf. Deliverable D9.6), all enabled by appropriate service metadata (cf. Deliverable D9.5). Hence, the ACGT data analysis environment can more correctly be described as the data analyst?s view of the integrated ACGT system. To complete the picture of the ACGT data analysis environment, this deliverable will focus on the actual knowledge discovery services that perform the actual data analysis. In ACGT, the open-source statistical toolkit / language R, the open-source suite of bioinformatics web-services BIOMOBY, and generic command-line tools have been identified as the most relevant tools for integration.
D7.1: Consolidated Requirements on ontological approaches for integration of multi-level biomedical information
This deliverable presents an analysis of the requirements needed in Work Package (WP) 7: Ontologies and Semantic Mediation Tools. It has been extended to provide a vision of the state of the art in some of the focused issues within WP7. A description of the approaches adopted, at the time of writing this document, has been included, as well as a complete requirements specification of the methods and tools to be investigated and developed during the next phases of the ACGT project.
The partners involved in WP7 have adopted a standard-based methodology for gathering requirements. It is based on specific scenarios provided by both technicians and end users. Such requirements can evolve during the entire project. They can be modified to follow up the evolution of the state of the art in the involved areas.
This document includes the ACGT Master Ontology on Cancer. This important objective for ACGT is described here to facilitate its understanding and use as a core resource for semantic mediation and interoperability.
D7.8: Introduction of a new clinical trial in ACGT: a case study
This deliverable aims at describing the experience of the inclusion of a new CT (at its early stages) in the ACGT platform. In this particular case, we despict an experimental scenario where data sets already exist before the begining of the trial. More concretely, the experiment deals with the integration of microarray (Arrayexpress) and relational clinical (SIOP) data. This document shows the process of setting up the new trial in the platform, describing the different components involved, and despicting results of the experiments carried out.
D7.9: Formal procedures and protocols for the semantic integration of clinical trials in ACGT
This deliverable aims at describing the procedures and protocols that need to be applied when a new clinical trial is added to the ACGT infrastructure. The final goal of the described steps is to offer clinicians the possibility to run and control a trial exclusively within the ACGT platform and, eventually, be able to combine that trial’s data with data from other trials. The presented procedures and protocols are based on the use of different tools and resources interacting with each other in order to make the mentioned features available to the user. An overview of those tools and resources, along with the involved procedures and protocols, is given in this document.
D8.1: Consolidated requirements (including information flows) of the in silico simulation models
The present deliverable outlines the requirements of the in silico oncology simulation models to be developed within the frame of workpackage WP8 of ACGT. An introduction to the notion of the "Oncosimulator" along with a number of high-level information flow diagrams and a brief description of the corresponding clinical trials constitute the core of the document.
The basic actions to be implemented are the following:
1. Development of the "Oncosimulator".
The constituent simulation models will be based on the novel, essentially "top-down" modeling approach developed by the In Silico Oncolog Group, ICCS, National Technical University of Athens.
2. Provision of pertinent clinical data for the two cases to be addressed, namely nephroblastoma (Wilm's tumour) and breast cancer. The in silico oncology trial will be based on the two clinical trials (nephroblastoma SIOP 2001/GPOH and breast cancer TOP trial) following their considerable enhancement in terms of data collection. It is pointed out that the design and
implementation of clinical trials in order to validate, adapt and optimize tumour behaviour models is a worldwide novelty.
3. Technical requirements (data handling, parallelization and grid
architecture usage, image processing, visualization).
Indicative references delineating the basis of the overall modeling philosophy to be adopted are also provided.
D8.4: Report on the clinical adaptation and validation procedure of the Oncosimulator and its integration into the ACGT architecture
The present document aims at both recapitulating the main features and modules of the ACGT Oncosimulator and providing a fairly comprehensive account of the latest work that concerns mainly the procedures of its clinical adaptation and validation. The integration of the Oncosimulator into the ACGT architecture is also dealt with. Both the scientific and the technological aspects of the endeavour are addressed. The document concludes with a critical evaluation of the Oncosimulator development and the process of its envisaged clinical translation.
D9.5: Report on the Final ACGT Workflow Environment - D9.6 Report on the Final specifica-tions of meta-data for the ACGT da-ta, tools, services and workflows
The present document is a merger of the deliverables 9.5 and 9.6. It offers a comprehen-sive description of the final ACGT workflow environment and the metadata specifications for the data, tools, services, and workflows. The design considerations, architecture, and implementation of the workflow management system are provided in sufficient detail. In the second part of the document the use of metadata annotations in ACGT is described in a unified view by consolidating input from previous deliverables.
D10.1: Production of informed-consent form in compliance with the clinical trials, post-genomic research and genetic data handling requirements
This deliverable contains in the first part an analysis of the relevant ethical and legal requirements for informed-consent forms within ACGT. Special issues such as the scope of the consent with special regard to future research, informed consents of minors and relatives are discussed.
The second part contains the general terms of ACGT, that have to be accepted by every participant, as well as different consent forms and agreements, that have to be concluded between the different participants.
D10.2: The ACGT ethical and legal requirements
This deliverable contains an analysis of the relevant ethical and legal requirements for ACGT.
The first part of this document analyzes the ethical requirements regarding clinico-genomic research within the ACGT architecture, especially with regard to informed consent and disclosure of research results. In order to protect patients' autonomy and their right to self-determination - the most basic principles to be respected in the context of medical research involving patients - the informed consent for participation in ACGT has to react in an appropriate manner to these challenges. In ethical terms, a tiered consent offering to donors the possibility to authorize a broader or more restricted range of research to be done with their samples and data and time frame they may be used for research would be preferable. However, this model is difficult to handle in practice.
Therefore, a model of consent referring to a purpose of intermediate scope (clinico-genomic research on cancer) in the context of a specific structure or project (ACGT) is proposed, which is within the limits of ethical as well as legal considerations. Concerning the disclosure of research results, it is widely agreed that general research results must accessible for research subjects regardless of the inalienable right of the patients to access his or her personal data. Since clinico-genomic research may also yield individually relevant results, it is additionally recommended that ACGT provides the technical and organizational means for individual feedback processes of such results.
The second part analyzes the legal requirements, particularly with regard to data protection and privacy. The goal to be achieved is to establish a structure where the competing aims of modern genetic research and the data protection needs of the participating patients can be met. Genetic data is very sensitive data which differs from ?normal? data in a crucial point: it cannot be anonymized completely and therefore falls under special requirements for data processing. In order to get as many data protection operations within ACGT outside the scope of the Data Protection Directive as possible, it is recommended to establish a Data Protection Architecture within the ACGT framework, which comprises a double pseudonymization procedure, the establishment of an ACGT Data Protection Board as central data controller and a Trusted Third Party.
Furthermore we analyze the impact of the Directive 2000/31/EC on E - commerce on ACGT. This analyzsis concerns the relationship between ACGT / physicians and researchers, dealing with service provider, users, contract by electronic means, etc. in the context of ACGT.
D10.6.2: First results of the international and national empirical survey on patients’ and parents’ perspectives and needs
This deliverable presents the first results of the international and national empirical survey on patients’ and parents’ of minor patients perspectives and needs regarding informed consent and data protection in clinical and clinico-genomic trials. The design of the survey was already described in detail in deliverables 10.5 and 10.6.1. This report presents first results of the German survey focussing on the attitudes and expectations of parents of oncologically treated children.
D11.4: Requirements and guidelines for developing secured ACGT services
This document defines the concept of an “ACGT enabled” service and specifies the security requirements that it must meet in order to obtain that label. Any service that wishes to process data protected by the ACGT data protection framework must comply with these requirements. Services of a more public nature are recommended to also comply with these requirements and guidelines.
D12.7: Final Report on the clinical benefits delivered by the ACGT project
This document presents the ACGT deliverable D12.7: Final Report on the clinical benefits delivered by the ACGT project. To evaluate the clinical benefits of ACGT, we have used the TOP trial as an example, as it will also be done in the final demonstration. This deliverable will present and discuss several procedures and tools set up during the ACGT project in the context of the TOP trial. In practice, this deliverable unfolds into eleven- (11) main chapters. The eight first chapters will describe some tools, procedures and results obtained in the context of the TOP trial and the final two chapters will report on conclusions and perspectives of ACGT.
D13.1 :Evaluation criteria and verification procedures of the ACGT platform
The present document provides a list of evaluation and validation procedures for the ACGT infrastructure. It is subdivided into two major parts. The first part provides recommendations for the development of quality procedures to ensure the quality of software in each technical work package. The actual QA procedures for the ACGT software components can be found on the BSCW document server. The access to software management tools made available is the context of ACGT is also described in the present document.
The second part provides evaluation criteria from the perspective of the end-user. The latter is focused on the ability of users to utilize the ACGT infrastructure to solve practical scenarios. The scenarios are tightly bound to the data architecture currently accepted they may and will evolve with the architecture of the system.
D14.7: The ACGT Educational Video Report
This document reports on the ACGT Video.
D15.6: Final report and analysis of project dissemination activities
The present document summarizes the dissemination activities undertaken by the ACGT project consortium during the four years of its implementation. Dissemination has been made through several means, from electronic distribution of newsletters and articles to publications and presentations at international relevant meetings with a strong coordination between the partners. This coordination has allowed the consortium to achieve more than just advertising or disseminating, but also enhanced the visibility of the ACGT platform and tools worldwide, thus demonstrating strongly that ACGT clinical trials pave the way to future applications in the healthcare domain.
D16.4: The ACGT Competition Report
This document reports on the ACGT Competition