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"Angeles R. de Cara" <[log in para visualizar]>
Reply To:
Foro sobre Fisica Estadistica <[log in para visualizar]>
Tue, 22 Jun 2004 12:27:19 +0100
TEXT/PLAIN (376 lines)
Issue's Topics:
        Course in Informatics for Biology 2005, Pasteur Institute
        Call for Papers - DIMACS Workshop on Reticulated Evolution
        New Keizer Text Website
        Position at the Anthropological Institute and Museum, Zrich
        Positions, MC-RTN Project
        Research Scientist, Biology/Molecular Biology
        NCI Seeks Tenured/Tenure-Track Viral Cancer Epidemiologist


From: Catherine Letondal <[log in para visualizar]>
Date: Wed, 16 Jun 2004 15:02:44 +0200
Subject: Course in Informatics for Biology 2005, Pasteur Institute

                Course in Informatics for Biology 2005

In the series of courses offered at the Pasteur Institute, a course will be
offered in informatics in biology. The next session will take place from
January to end of April 2005.

The main goal of this course is to provide researchers in biology an initial
exposure to informatics. Admission to the course is reserved for those with a
degree in biology or a related discipline.

With more and more bioinformatics tools available, it becomes increasingly
important for researchers in biology to be able both to manage their data,
implement their ideas, and judge for themselves the usefulness of new
algorithms and software.

This course will emphasize fundamental aspects of computer science and apply
them to biological examples. Theoretical aspects (algorithm development,
logic, problem modeling and design methods), and technical applications
(databases and web technologies) that are relevant for biologists will be
thoroughly discussed.

Programming is presented through the object-oriented paradigm, using a modern
high-level language, Python, provided with tools for biology and enabling
both prototyping or scripting and the building of important software systems.
Learning of additional languages (perl and C) will be available for
interested students.

Learning during the course will be reinforced with computing exercises, and
effective training will be provided by a 2 month research project.

The working language of the course is French.

For further information, please consult:


Catherine Letondal -- Pasteur Institute Computing Center


From: Linda Casals <[log in para visualizar]>
Date: Mon, 14 Jun 2004 11:22:48 -0400 (EDT)
Subject: Call for Papers - DIMACS Workshop on Reticulated Evolution

DIMACS Workshop on Reticulated Evolution

Call For Papers

September 20 - 21, 2004
DIMACS Center, CoRE Building, Rutgers University


  Mel Janowitz, DIMACS, [log in para visualizar]
  Randy Linder, University of Texas, [log in para visualizar]
  Bernard Moret, University of New Mexico, [log in para visualizar]

Presented under the auspices of the Special Focus on Computational
       Molecular Biology.

Announcing a workshop on reticulated evolution to be held September
20-21, 2004. Registration details and further information for the
workshop may be obtained from the website

Here is a brief description of the goals of the workshop.  Species
evolution has long been modeled as a branching process that can
uniquely be represented by a tree topology. In such a topology, each
species can only be linked to its closest ancestor, while interspecies
relationships such as species hybridization or lateral gene transfer
in bacteria are not allowed. With the advent of phylogenetic analysis
at the molecular level, there is increasing evidence that such a model
is inadequate. This workshop will explore the history and latest
status of these new models of "reticulate evolution", and will be
coupled with a smaller working group meeting designed to explore
promising avenues for future research.

Call For Papers

The organizers welcome contributed papers that are in the spirit of
the above announcement. Abstracts may be submitted to any of the
organizers no later than August 1, 2004. Any submissions must be
approved by the organizers.


 Pre-registration deadline: September 13, 2004

Please see website for additional registration information.


From: Chris Fall <[log in para visualizar]>
Date: Fri, 18 Jun 2004 14:47:31 -0500
Subject: New Keizer Text Website


Our colleague John Wagner has completely revised the website accompanying the
Computational Cell Biology (Springer Verlag, 2002)

We are also pleased to announce that there will be a third, corrected
printing this summer. (Royalties from this text are donated to the Joel E.
Keizer memorial endowment for collaborative interdisciplinary research in the
life sciences.)

Contents of the Web Site include:
- XppAut and MATLAB code for the replication of many of the figures
- a link to the Virtual Cell implementation of many covered models
  (thanks to Dr. Les Loew and Johann Cutiongco)
- a list known errors in the first and second printings
- contact information for Authors and Editors
- useful links for the community

In the near future we expect to add:
- all of the figures from the book for use in teaching
- an online version of a solutions manual currently being developed

This is an ongoing project and we are hopeful that this site will evolve into
a useful resource for those interested in Computational Cell Biology. We
would like to SOLICIT additional teaching materials related to the textbook
such as Powerpoint presentations or PDF's, additional useful links, and any
other suggestions.

About "Computational Cell Biology:"
Tim Elston, Bard Ermentrout, Chris Fall, Jim Keener, Joel Keizer, Yue-Xian
Li, Eric Marland, Alex Mogilner, Bela Novak, George Oster, John Pearson, John
Rinzel, Artie Sherman, Greg Smith, John Tyson, John Wagner and Hongyun Wang

Computational Cell Biology provides an introduction to dynamic modeling in
cell biology, emphasizing computational approaches based on realistic
molecular mechanisms. It is designed to introduce cell biology and
neuroscience students to computational modeling, and applied mathematics
students, theoretical biologists, and engineers to many of the problems in
dynamical cell biology. The concept for such a textbook was conceived of and
begun by Professor Joel Keizer based on his many years of teaching and
research together with his colleagues.  The project was expanded and finished
by his students and friends after his untimely death in 1999.

Carefully selected examples are used to motivate the concepts and techniques
of computational cell biology, through a progression of increasingly more
complex and demanding cases. Illustrative exercises are included with every
chapter, and mathematical and computational appendices are provided for

This textbook will be useful for advanced undergraduate and graduate
theoretical biologists, neuroscientists, engineers and for mathematics
students and life scientists who wish to learn about modeling in cell

Evaluation copies are available for loan directly from Springer-Verlag.

Chris Fall, Eric S. Marland, John M. Wagner and John J. Tyson


From: Carel van Schaik <[log in para visualizar]>
Date: Wed, 16 Jun 2004 17:26:19 +0200
Subject: Position at the Anthropological Institute and Museum, Zrich

The Anthropological Institute and Museum at the University of Zrich,
Switzerland, is inviting applicants for the position of "Oberassistierenden
100%" in the area of Mathematical Biological Anthropology or Primatology.

The position is for a maximum of 6 years, and is available as of September 1,
2004.  The successful candidate is expected to:
-  Develop and implement models of socioecological, cognitive, cultural
and life history evolution in primates
-  Participate in the empirical evaluation of the models, including
statistical analyses
-  Participate in teaching at the Institute, especially in the area of
Modeling and Research Methods
-  Mentor undergraduate, master^s and graduate student projects that involve
modeling or analysis

The successful candidate has a PhD in a relevant area, is well versed in
biological mathematics, and has experience with evolutionary modeling,
preferentially of issues in primatology or biological anthropology, or a
demonstrable willingness to familiarize themselves with the subject matter;
as well as the ability to teach in German or a demonstrable willingness to
learn to do so within two years.

The appointment is at the level of Oberassistent; salary and benefits are in
accordance with the regulations of Kanton Zrich.

Send your full application (CV, list of publications, addresses of three
referees) before July 12 to Prof. Carel van Schaik, Universitt Zrich,
Anthropologisches Institut und Museum, Winterthurerstrasse 190, 8057 Zrich,
Switzerland.  For additional information, please contact Ms. Claudia
Zebib-Brunner, Tel. ++41 (0) 1 635 54 11, e-mail: [log in para visualizar]


From: Luigi Preziosi <[log in para visualizar]>
Date: Thu, 17 Jun 2004 13:57:31 +0200
Subject: Positions, MC-RTN Project

The Marie Curie Research Training Network (MC-RTN) project

"Modelling Mathematical Methods and Computer Simulation of Tumour Growth and

has been successful in obtaining funding from the European Community under
its 6th Framework Programme.

The twelve partners of the Network cover nine countries:

- France (Universite J. Fourier, Grenoble I, CNRS and Ecole Normale
Suprieure, Paris)
- Germany (University of Dresden and University of Witten/Herdecke)
- Greece (Foundation for Research and Technology, Crete)
- Israel (IMBM: Institute for Medical Bio-Mathematics)
- Italy (Politecnico di Torino)
- Poland (University of Warsaw)
- Spain (Universidad Complutense de Madrid)
- Sweden (Goteborg University)
- United Kingdom (University of Nottingham and University of Dundee)

The aim of the Marie Curie Research Training Network is to develop the whole
modelling process from phenomenological observation to simulation and
validation, through the development of mathematical models and their
qualitative and quantitative study, in order to simulate the different
aspects of tumor dynamics within the full range of scales (sub-cellular,
cellular and macroscopic), including multiscale aspects.  The primary
objective is to promote training-through-research, especially of young
researchers having less than ten years of research experience at the
pre-doctoral and post-doctoral level, respectively denoted in the table below
by ESR (Early Stage Researcher) and ER (Experienced Researcher). Community
funding will cover the temporary appointment of young researchers coming from
a country other than that of the team concerned and the organisation of
summer schools and workshops.

The available positions and reference e-mail addresses are listed below

- Paris (France)
ESR for 11 months, ER for 22 months: [log in para visualizar]

- Grenoble (France)
ESR for 36 months, ER for 12 months: [log in para visualizar]

- Witten-Herdecke (Germany)
ESR for 36 months, ER for 12 months: [log in para visualizar]

- Dresden (Germany)
ESR for 18 months, ER for 18 months: [log in para visualizar]

- Crete (Greece)
ESR for 24 months, ER for 24 months: [log in para visualizar]

- IMBM (Israel)
ESR for 12 months, ER for 24 months: [log in para visualizar]

- Turin (Italy)
ESR for 24 months, ER for 24 months: [log in para visualizar]

-Warsaw (Poland)
ESR for 36 months, ER for 24 months: [log in para visualizar]

- Madrid (Spain)
ESR for 3 months, ER for 18 months: [log in para visualizar]

- Goteborg (Sweden)
ESR for 11 months, ESR for 36 months: [log in para visualizar]

- Dundee (UK)
ESR for 18 months, ER for 18 months: [log in para visualizar]

- Nottingham (UK)
ESR for 18 months, ER for 18 months: [log in para visualizar]

More information can be found at the web page:
or contacting [log in para visualizar] or any of the addresses above.


From: Irena Johnson <[log in para visualizar]>
Date: Thu, 17 Jun 2004 12:36:56 -0400
Subject: Research Scientist, Biology/Molecular Biology

Research Scientist, Biology/Molecular Biology

Gene Network Sciences invites applications from exceptional scientists with
experience in molecular immunology and inflammation to help create
large-scale data driven simulations of acute inflammatory response and skin
sensitization. Successful candidate would have an interest in integrating
genomics and proteomics data to create comprehensive models of the cell.
Responsibilities involve reviewing relevant biological literature and
databases to develop large-scale graphical molecular level models of cancer
cells, communicating with mathematical modelers to create dynamical
simulations, designing experiments and testing the simulations.


Applicants must have a Ph.D. in immunology, molecular immunology or related
discipline. Good communication skills are required, as well as expertise in
high-throughput genomic and proteomic experimental methods (including
experience in at least one of the following: microarrays, mass spectrometry,
siRNA, yeast-two hybrid). Extensive knowledge of the gene expression
networks, signal transduction pathways, and other pathways underlying
inflammation is highly desired. US citizenship or work permit is strongly

To apply for this position:

1) E-mail [log in para visualizar] with the subject "Immunologist-S".

2) Include your resume as either Word or PDF file in the attachment.

3) Do not include cover letter or any other additional information or
attachments in your e-mail.


From: Raymond Mejia <[log in para visualizar]>
Date: Wed, 16 Jun 2004 08:40:16 -0400
Subject: NCI Seeks Tenured/Tenure-Track Viral Cancer Epidemiologist

National Cancer Institute Seeks
Tenured/Tenure-Track Viral Cancer Epidemiologist

The Viral Epidemiology Branch, NCI, is searching for a tenure-track or
tenured investigator to join their epidemiologic research program focused on
human cancer risk related to infection with viruses or other agents.
Candidates should have an M.D., Ph.D. or equivalent doctoral degree; and must
have substantial experience in human viral or cancer epidemiology, including
design, conduct and analysis of epidemiologic studies. They also must have a
sound working knowledge of basic statistical methods and oncogenic human
viruses or bacteria, as well as the diseases they cause. A substantial record
of publication in the peer-reviewed medical or scientific literature that
demonstrates their knowledge, skills, and ability to conduct
multidisciplinary collaborative epidemiologic research is required.
Candidates must also display strong leadership in independent, innovative
research. They should also have strong communication skills for writing
research papers, presenting at scientific meetings, and collaborating with
NIH intramural and extramural scientists.

Applicants should send a cover letter that briefly summarizes their research
interests, experience, and accomplishments; C. V., with bibliography; copies
of three selected publications; and three letters of reference (either
included with the package or sent directly by the recommender) to: Chair,
Search Committee, Viral Epidemiology Branch, NCI c/o Mrs. Judy Schwadron,
DCEG, NCI, Executive Plaza South, Rm. 8073, Bethesda, MD 20892.