KRDB Research Centre
for Knowledge and Data
 



Computer Science and IT with/for Biology

An interdisciplinary Seminar Series

CSBio Reader: Extended abstracts

Introduction

The vibrant and emerging research area of "doing research and engineering in the subject domain of biology and the applied biosciences" comprises one or more (sub-) disciplines of computer sciences and information technology that can be mixed with any of the (sub-) disciplines in biology, ecology, and applied biosciences (such as medicine and agriculture). Depending on the emphasis, this combination tends to favour one or more of the following terms to indicate the type of activity: Computational Biology, Systems Biology, Bioinformatics, In Silico Biology, Ecoinformatics, (Bio)Medical Informatics, and bio-ontologies, among others.

But what exactly is the breadth and depth of these relatively new fields, and what are its characterstic activities? What is, or can be, used from mathematics to advance biology at a faster pace? What type of problems do bioscientists perceive that need to be solved? Is engineering only a supportive discipline for biology? If not, where and how is biology pushing the frontiers of computer science and IT? How did, and does, the combination of computer science & biology lead to landmark achievements - and which ones are considered to be achievements?

Against this background, the KRDB Research Centre of Faculty of Computer Science at the Free University of Bozen-Bolzano aims to present and form new expertises and professional profiles who can answer the growing demands of the biosciences and ultimately our societies in the area of using both theoretical and applied aspects of computer science and engineering, thereby contributing to pushing the frontiers in computer science as well as (applied) biology. To this end, it organizes the CSBio Seminar Series.

Aim and coverage of the seminar series:

The aim of the seminar series for the Trentino & (South) Tirol regions is to provide a broad spectrum of achievements, opportunities, and challenges on using/combining computer science with/for biology, highlighting diverse foci and approaches traversing biology (sub-) disciplines and applied bioscience and a wide range of computer science approaches.

This coverage goes from basic biosciences, such as genetics & cellular processes and larger systems in ecology, and the applied biosciences medicine and agriculture, to CS/IT fields of ontology/ies, logic, mathematics, NLP, database integration, and software development. Also ethical aspects concerning the achievements and prospects of combining biology with CS/IT will receive attention.

For more information, please contact:

Marijke Keet
keet at inf.unibz.it
(+39) 0471 016 128
        or
Enrico Franconi

(+39) 0471 016 120


October   November   December 

Date Time SpeakerAffiliationTitleAbstractSlides
October, 20th 16,00-17,00 Marijke Keet KRDB, FUB Current characteristics and historical perspective of CS & IT with/for Biology Abstract
pdf
October, 28th 16,00-17,00 Heiner Fangerau Heinrich-Heine-University Düsseldorf Finding Bioethical Literature - Databases and Data-biases Abstract
pdf
November, 9th 16,00-17,00 Alberto Policriti University of Udine Formal Tools for Systems Biology Abstract
pdf
November, 16th 16,00-17,00 Marco Roos University of Amsterdam Towards a virtual laboratory for integrative bioinformatics research Abstract
pdf (6MB)
November, 25th 16,00-17,00 Marie-Paule Lefranc LIGM, University of Montpellier A standardized and dynamic approach for immunogenetics and immunoinformatics: IMGT-Choreography based on the IMGT-ONTOLOGY concepts Abstract
pdf (6MB)
November, 30th 16,00-17,00 Sarah Cohen-Boulakia LRI, Paris BioGuide: A User-centric approach for querying biological data Abstract
pdf
December, 6th 16,00-17,00 Werner Ceusters ECOR, Saarland University Requirements for natural language understanding in referent-tracking based electronic health records Abstract
ppt (4MB)
December, 15th 16,00-17,00 Aldo Gangemi LOA-CNR, Rome Applying ontology design patterns to practical expertise: roles, tasks and techniques in the agricultural domain Abstract



October ^


October 20th , 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

Current characteristics and historical perspective of CS & IT with/for Biology
Marijke Keet, KRDB Research Centre for Knowledge and Data, Free University of Bozen-Bolzano, Italy


Although the emerging discipline(s) involved in combining CS/IT with biology may seem a new development, several historical aspects already can be identified. These, with its past and present characteristics, will be presented and discussed. Together, they provide a general introduction covering the breadth of the research topics of CS/IT with/for biology and its related applied life sciences, and offer a background framework to place the subsequent specialist seminars in its appropriate context.


October 28th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

Finding Bioethical Literature - Databases and Data-biases
Heiner Fangerau, Institute for the History of Medicine, Heinrich-Heine-University Duesseldorf, Germany


The selection of suitable databases for finding medical ethics literature is often difficult. There exists a great variety of electronic bibliographies listing medical ethical literature. These databases follow different quality standards. The quality standards applied by the databases as well as their selection of articles to be indexed have a strong effect on the user’s research results. Recent studies could show that there seems to be a regional bias in the most popular databases favouring US American periodicals compared to European literature on Medical Ethics. Especially this regional bias or other language or national biases can have an influence on ethicists research results. Examples from hot ethical issues like stem cell research, its ethical and legal evaluation and its representation in electronic bibliographies will be displayed to show of which data-biases researchers in ethics have to be aware. Solutions to overcome these biases will be presented.


November 9th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

Formal Tools for Systems Biology
Alberto Policriti, Dipartimento di Matematica e Informatica, University of Udine, Italy


In this talk we will illustrate the idea of exploiting formal models and languages used in software formal verification, with as aim the design of innovative systems to be applied in Systems Biology.
We will start by briefly describing the Simpathica tool (Simulation of Pathways and Integrated Concurrent Analysis), integrating mathematical and logical approaches for the study biochemical networks. We will continue with an overview of other possibilities to apply formal tools to cell biology. We conclude with addressing some algorithmic and expressivity issues, problems related with the use of standard/hybrid automata, and logical languages in the context of Systems Biology.

November ^


November 16th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

Towards a virtual laboratory for integrative bioinformatics research
Marco Roos, MicroArray Department, Integrative Bioinformatics Unit, University of Amsterdam, the Netherlands


The development of a virtual laboratory (VL) for integrative bioinformatics research will be discussed. This envisioned VL supports multi-disciplinary collaboration and interactive experimentation, and the experimental research cycle is empowered by a 'semantic framework' based on Semantic Web technologies that enables integration of data, information, and knowledge, including the results from intermediate steps in the VL. Our approach is 'case study'-driven in the sense that investigating a biological case is performed concurrently with the development of bioinformatics methodologies. Biological cases include, among others, transcription regulation & the histone code, and Huntington's disease.


November 25th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

A standardized and dynamic approach for immunogenetics and immunoinformatics: IMGT-Choreography based on the IMGT-ONTOLOGY concepts
Marie-Paule Lefranc, Laboratoire d'ImmunoGénétique Moléculaire, Université Montpellier II, Institut Universitaire de France, Institut de Génétique Humaine, IGH, UPR CNRS 1142, France


IMGT, the international ImMunoGeneTics information system® (http://imgt.cines.fr), is a high quality integrated resource specialized in immunoglobulins, T cell receptors, major histocompatibility complex, and related proteins of the immune system. IMGT contains 5 databases, 9 specific interactive tools and 8,000 HTML pages of synthesis and knowledge. I will describe how IMGT-ONTOLOGY, the first ontology in immunogenetics, provides genome, proteome and structure data standardization, and allows knowledge management by immunoinformatics. IMGT-ONTOLOGY concepts are available for the biologists and IMGT users in the IMGT Scientific chart, and for the computing scientists in IMGT-ML. IMGT-ML includes an XML Schema for each IMGT-ONTOLOGY concept and is used by IMGT Web services to exchange IMGT data. This is the first step towards the implementation of IMGT-Choreography, the bioinformatics process of complex immunogenetics knowledge.


November 30th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

BioGuide: A User-centric approach for querying biological data
Sarah Cohen-Boulakia, Laboratoire de Recherche en Informatique, CNRS-Université Paris-Sud, France


Life sciences are continuously evolving so that the number and size of new sources providing specialized information in biological sciences have augmented significantly in the last few years, as well as the number of tools required to carry out bioinformatics tasks. As a consequence, scientists are increasingly confronted with the problem of selecting appropriate sources and tools.
To address this problem, we have designed BioGuide, a user-centric framework that helps scientists choose sources and tools according to their preferences and strategy. BioGuide allows the user to specify his/her query through a user-friendly visual interface

December ^


December 6th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

Requirements for natural language understanding in referent-tracking based electronic health records
Werner Ceusters, European Centre for Ontological Research, Saarbrücken, Germany


Most electronic patient records contain identifiers to uniquely identify entities such as the patient, the physician, and the healthcare facility. None, however, contains thus far identifiers that uniquely identify the particular disorders patients have, the symptoms they experienced, the actual treatments that have been applied, and so forth. Referent tracking has been introduced as a paradigm to make this also a standard procedure. In this talk, we discuss how natural language understanding can contribute to this.


December 15th, 16:00-17:00 - Faculty of Computer Science, FUB, Seminar Room (first floor left)

Applying ontology design patterns to practical expertise: roles, tasks and techniques in the agricultural domain
Aldo Gangemi, Laboratory of Applied Ontology (LOA-CNR), Rome, Italy


Ontology design patterns help building a rationale for ontology construction, mapping, and evaluation. They are reusable components, but they also contribute to the formalization of relevant expertise in a domain for some task. Within the Agricultural Ontology Service project at UN agency FAO, some patterns of varied logical types have been applied in order to migrate legacy taxonomies, and to capture the expertise for large information service design. The most challenging representation issues concern roles, tasks, techniques, regulations, warning guidelines, etc., which required a complex design pattern based on a semantics for reified social objects. In the seminar I introduce the issues, methods and models employed in the creation of a large Fishery Ontology.




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