Open position in
Informatics/Bioinformatics
Crop Development Centre
University
of Saskatchewan
College of Agriculture and Bioresources
September
7, 2012
A 2-years Engineer position in
Informatics/Bioinformatics:
This position is funded by a
research grant administered by the
University of Saskatchewan
under the direction of Dr. C Pozniak, Crop
Development Centre,
College of Agriculture and Bioresources.
Background
In
support of the international effort (IWGSC -
http://www.wheatgenome.org/)
to
obtain a reference sequence of the bread wheat genome and to
provide
plant communities dealing with large and complex genomes
with a
versatile, easy-to-use online automated tool for
annotation, we have
developed the TriAnnot pipeline
(http://www.clermont.inra.fr/triannot).
Its
modular architecture allows for the annotation and masking
of
transposable elements, the structural and functional annotation
of
protein-coding genes with an evidence-based quality indexing,
and for
identification of conserved non-coding sequences and
molecular
markers. The TriAnnot pipeline is parallelized on a 712
CPU computing
cluster that can run a 1-Gb sequence annotation in
26 hours. It is
accessible through a web interface for small scale
analyses (< 100
sequences of 3Mb max) or through a server for
large scale annotations
(thousands of scaffolds). The performance
of TriAnnot was evaluated in
terms of sensitivity, specificity,
and general fitness using curated
reference sequence sets from
rice and wheat. In less than 8 h, TriAnnot
was able to predict
more than 83% of the 3,748 CDS from rice chromosome 1
with a
fitness of 67.4%. On a set of 12 reference Mb-sized contigs
from
wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of
the
genes among which 54% were perfectly identified in accordance
with the
reference annotation. It also allowed the curation of 12
additional
genes based on new biological evidence, increasing the
percentage of
perfect gene prediction to 63%. TriAnnot was
designed specifically for
complex genomes like wheat, and
systematically showed a higher fitness
than other annotation
pipelines. TriAnnot is easily adaptable to the
annotation of other
plant genomes, and should become a useful resource
for the
annotation of large and complex genomes in the future.
However,
there is a need for further improvements:
- Build a virtual
machine of the TriAnnot pipeline;
- Improve the Gene
modeling process - definitely make a choice between
two combiners: Eugene and Augustus;
- Incorporate new, well
trained ab initio gene prediction programs;
- Develop tools
to display splicing variants;
- Implement a module for the
discovery of SNP markers;
- Develop and incorporate three
new panels:
o mapping the gene models on
selected genome models
o mapping the gene
models within a pre-calculated phylogeny tree
o
mapping the gene models within a known biological pathways;
o evaluate the possibility to develop a "bogas-like"
interface for
wheat manual curation
(see
http://bioinformatics.psb.ugent.be/webtools/bogas/).
Building
a virtual machine is a high priority as the improved
TriAnnot
pipeline will be installed as a mirror site to improve
the informatics
infrastructure in Canada. In this respect, we
would develop a
collaboration with iPlant to install the TriAnnot
virtual machine
(TriAnnot-VM) within the iPlant cyber
infrastructure located in the
USA. Collaborations are already
underway with the CNRS at Roscoff
(C. Caron) and the IBCP at Lyon
(C. Blanchet) to work on these
aspects. The engineer hired for
this position will be in contact with
these different centers to
build the virtual machine.
The development of the "bogas-like"
interface will be made in
close collaboration with the VIB in
Ghent, Belgium.
Research Groups
The candidate will work
under the direction of Dr. C. Pozniak,
University of
Saskatchewan.
The successful candidate will spend the first
year as a Visiting
Scientist in the group "Structure,
Function and Evolution of the Wheat
Genome" led by C.
Feuillet and located at the UMR INRA-UBP GDEC in
Clermont-Ferrand
(France). She/he will improve further the TriAnnot
pipeline (see
above) and build the TriAnnot-VM in direct collaboration
with P.
Leroy, the research engineer in charge of the TriAnnot project
in
the group. She/he will interact with researchers and
graduate
students that are users of the pipeline. She/he will also
interact with
other groups involved in Genetics, Bioinformatics
and with other
international laboratories developing similar
activities.
In the second year of the project, the candidate
will work at the Crop
Development Centre, University of
Saskatchewan, Canada in the research
group led by Dr. Pozniak.
She/he will install and test the TriAnnot-VM
within the
informatics infrastructure available at the University
of
Saskatchewan and use it to annotate the sequence of wheat
chromosomes
being sequenced by that group. The second year of the
project will
involve interaction with iPlant to install the
TriAnnot-VM within the
iPlant cyber infrastructure in US. The
successful candidate will also
assist with writing and preparation
of manuscripts for publication.
Qualifications Required
The
candidate must have a minimum of a Master's degree in
computer
science or a related field with at least three years of
bioinformatics
experience. The candidate should have a good
knowledge in Perl, python
and Object Programming. Previous
experience of Perl Object Oriented
Programming is recommended.
Candidate has to be familiar with parallel
programming (Cluster)
and Cloud computing. Research experience in plant
genomics is
desirable.
Applicant must have a clear evidence of
productivity, creativity and
independence; excellent communication
skills, and must be proficient in
both reading and writing in the
English language and an ability to work
both independently and
within a team. Candidates must have demonstrated
report writing
and publication capabilities.
Salary: A competitive salary is
available with full benefits (pension,
health & dental, life
insurance). Salary will be commensurate with
experience.
The
University of Saskatchewan is committed to employment equity
and
applications from women, aboriginal peoples, visible
minorities and
persons with disabilities are encouraged. All
qualified individuals are
invited to apply, but Canadian citizens
and permanent residents will be
given priority.
Contacts
Parties
interested in the position should provide by email a letter
of
application, Curriculum Vitae with a publication list, a brief
statement
of research and interests, and the names and contact
information for at
least three references, to:
Chris
Barker
Genome Prairie
Senior Project Manager
Room 2E80,
Agriculture Building
Department of Plant Sciences
University of
Saskatchewan
Saskatoon, Saskatchewan
S7N
5A8
cbarker@genomeprairie.ca
Review
of applications will begin September 15th, 2012 and continue
until
the position is filled. All applicants will be notified
shortly
thereafter.
The preferred start date for the
position is November 1st, 2012.