*Open position: Assistant Professor Bioinformatics*
The Theoretical Biology & Bioinformatics (TBB) group at Utrecht is
searching for an assistant professor in bioinformatics with a track
record reflecting exciting biological research. You will be functioning
at the PI level, develop your own research line and supervise your own
PhD students. Your background could be in biology provided you have a
solid expertise in bioinformatics, or your background could be in
computer science or physics provided you have a genuine biological
research line.
You are expected to develop your own research line in the life sciences
using bioinformatics approaches. This involves acquisition of grants to
form your own group within the Bioinformatics group. Assistant professor
positionsinvolve both research and teaching. You will be expected to
participate in existing bioinformatics courses at the bachelor/master
levels and to participate in the development of a new advanced
bioinformatics course.
The staff researchers of theoretical biology and bioinformatics at the
biology department use mathematics, computer science and bioinformatics
to perform fundamental biological research in a variety of biological
disciplines. Currently it is seeking to strengthen its bioinformatics
research. The bioinformatics group develops novel bioinformatics
approaches in the areas of comparative genomics and data integration to
pursue research into evolution, signalling networks and plant
bioinformatics. The group is part of the Institute of Biodynamics and
Biocomplexity (IBB), embedded in one of the largest Biology departments
in the Netherlands (>200 new students per year). The group teaches
bioinformatics to biology students at the bachelor and master level. PhD
students in the group have diverse backgrounds ranging from biology,
chemistry to computer science, and typically half of them are from
abroad. The IBB focuses on molecular life sciences, and is collaborating
with other departments of the Faculty of Science, the Faculty of
Medicine, and the Hubrecht Institute in Utrecht.
To apply, please find the position here
<http://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Por…>and
attach a letter of motivation, a concise (half page) research plan and
curriculum vitae. As part of the selection procedure successful
candidates are expected to give an outline of his/her research plans in
a written report and an oral presentation. The application deadline is
December**1^st , 2013.Additional information about the vacancy can be
obtained from: dr. B. Snel (b.snel(a)uu.nl)
Conditions of employment: The candidate is offered a full-time position
on a tenure track basis at the assistant professor level. The tenure
track period is for 5 years, and after a successful evaluation this will
be continued on a permanent basis. The salary is supplemented with a
holiday bonus of 8% and an end-of-year bonus of 8.3% per year. In
addition we offer: a pension scheme, a partially paid parental leave,
flexible employment conditions. Conditions are based on the Collective
Labour Agreement Dutch Universities. The research group will provide the
candidate with necessary support on all aspects of the project. The
gross salary is in the range between 3227 and maximum 5979 Euro per month.
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The 2nd International Conference on the Theory and Practice of Natural
Computing (TPNC 2013) invites authors to submit poster presentations. TPNC
2013 will be held in Cáceres (Spain) on 3-5 December, 2013. See
http://grammars.grlmc.com/tpnc2013/
Poster presentations are intended to enhance informal interactions with the
conference participants, at the same time permitting in-depth discussion.
TOPICS
Authors are encouraged to submit presentations that discuss novel work in
progress on:
- nature-inspired models of computation,
- synthesis of nature by means of computation,
- nature-inspired materials,
- information processing in nature,
- applications of natural computing.
Posters do not need to present final research results. Work that may lead to
new interesting developments is welcome.
KEY DATES
Submission deadline: October 20, 2013
Notification of poster acceptance or rejection: October 27, 2013
SUBMISSION
Please submit a .pdf abstract through:
https://www.easychair.org/conferences/?conf=tpnc2013
It should contain the title, author(s) and affiliation, and should not
exceed 500 words.
PRESENTATION
Posters will be allocated 8 minutes each in the programme for oral
presentation. Moreover, they will remain hanging during the whole conference
for discussion.
PUBLICATION
Posters will not appear in the LNCS proceedings volume of TPNC 2013.
However, they will be eligible for submission to the post-conference Soft
Computing journal special issue.
REGISTRATION
Authors of accepted posters have to register to the conference. Their
registration fare is reduced: 150 Euro (appr. one third of the fare for PhD
students).
Course Announcement
NOTE: please apply as soon as possible, the period for applications is
exceptionally short due to operational reasons
*ARANGS13*
Automated and reproducible analysis of NGS data
IMPORTANT DATES for ARANGS13
Deadline for applications: October 8th 2013
Notification of acceptance dates: October 15th 2013
Course date: October 21st - October 24th 2013
Course Description:
Next generation sequencing (NGS) technologies for DNA have resulted in
a yet bigger deluge of data. Researchers are learning that analysing
such data sets is becoming the bottleneck in their work. In many
cases, several steps in these analyses are fairly generic (e.g.
quality control filtering, alignment to reference sequences, typing)
so that off-the-shelf pipelines can be applied. In other cases, novel
research approaches require development of new analysis pipelines.
Either way, all analysis steps should be repeatable and any changes
made to the data (e.g. renaming, annotation, alignment) should be
recorded so that the provenance of the results is clear and inferences
are reproducible. In this brief workshop we will establish several
best practices of reproducibility and provenance recording in the
(comparative) analysis of data obtained by NGS. In doing so we will
encounter the commonly used technologies that enable these best
practices by working through use cases that illustrate the underlying
principles. Building on the basis of workflow development, we will
further illustrate how custom-built workflows can be manipulated using
graphical platforms (e.g. Galaxy, Taverna, etc.).
Best practices
Standardized project organization
Projects 'runnable' without user intervention
No loss of data, metadata, parameters or source code through versioning
Sharing of scripts and workflows
Technologies
Next generation sequencing platforms
File formats (e.g. FASTQ, SAM/BAM, GFF3)
Command-line executables, command line scripting and batching
High-level programming with domain-specific toolkits
Revision control systems
Workflow environments (both visual and command line)
Use cases
Phylogenetic placement of metagenomic data
Typing of pathogens
Comparative analysis of multicellular genomic data
Post-assembly: handling richly annotated genomes
More information, including application instructions, available at
http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS13/
Thank you
Pedro Fernandes
GTPB coordinator
--
Pedro Fernandes
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt
_______________________________________________
Gtpb mailing list
Gtpb(a)igc.gulbenkian.pt
https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb
BBC2013 – BeNeLux Bioinformatics Conference 2013
Date: December 9 & 10, 2013
Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium
Website: http://bbc2013.ibsquare.be
Abstract submission deadline: October 6, 2013 (extended)
Early registration deadline: November 8, 2013
Dear Colleagues,
Due to multiple requests, the deadline for submitting abstracts to the 8th edition of the BeNeLux Bioinformatics Conference has been extended to October 6, 2013!
Note that we introduced the possibility to submit late abstracts within October 20, but that they will be considered only for poster presentation.
The theme of this year's conference is: "Bioinformatics at all scales of life".
Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org)
Call for abstracts
We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation.
Contributions from all fields of bioinformatics are welcome and encouraged.
We have provided a template to use for submission through the EasyChair system: https://www.easychair.org/conferences/?conf=bbc2013 .
Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts .
We hope to see you all in Brussels!
--
The BBC 2013 organising committee
BeNeLux Bioinformatics Conference 2013
December 9-10, 2013 (Brussels)
