----------------------------------------------------
Subject: SMB Digest v13i29
SMB Digest July 17 2013 Volume 13 Issue 29
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
http://www.smb.org/ .
Access the Bulletin of Mathematical Biology, the official journal of
SMB, at http://www.springer.com/11538 .
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
New NSF Proposal Requirements
Conference: PDEs and Dynamical..., Sep 30 - Oct 3, Bar Ilan U
PhD Positions: Computational & Systems Biology, Lisbon & Lyon
Post-doc: Mathematical Ecology, Monash U, Australia
Post-doc: Theoretical Immunology, Imperial College London
Post-doc: Math with Applications in..., Johannes Gutenberg U
Post-docs: Computational & Systems Biology, Lisbon & Lyon
Job Openings: Co57 Systems, Cambridge, MA
First Release of StochSS: Stochastic Simulation Service
SMBnet Reminders
----------------------------------------------------
From: Tie Luo <tluo@NSF.GOV>
Date: July 16, 2013 12:40:32 PM
Reply-To: dmsnews <DMSNEWS@LISTSERV.NSF.GOV>
Subject: New NSF Proposal Requirements
The National Science Foundation has made changes to the Grant Proposal
Guide (GPG) to implement the recommendations of the National Science
Board. The link to the new GPG is:
http://www.nsf.gov/pubs/policydocs/pappguide/nsf13001/gpg_index.jsp
There are a few key changes that we would like to bring to your
attention. Please note that proposals that do not address these
requirements will be returned without review.
* Project Summary (II.C.2.b): "Each proposal must contain a summary of
the proposed project not more than one page in length. The Project
Summary consists of an overview, a statement on the intellectual merit
of the proposed activity, and a statement on the broader impacts of the
proposed activity."
FastLane has been modified to display three separate text boxes in which
proposers must provide an Overview and address the "Intellectual Merit"
and "Broader Impacts" of the proposed activity. Proposals that do not
separately address the overview and both merit review criteria within
the one-page Project Summary will be not be accepted or will be returned
without review.
* Project Description: Section on Broader Impacts (II.C.2.d.): "The
Project Description must contain, as a separate section within the
narrative, a discussion of the broader impacts of the proposed
activities."
* Project Description: Results from Prior NSF Support (II.C.2.d.iii):
"If any PI or co-PI identified on the project has received NSF funding
(including any current funding) in the past five years, information on
the award(s) is required, irrespective of whether the support was
directly related to the proposal or not. Funding includes not just
salary support, but any funding awarded by NSF. Each PI and co-PI who
has received more than one award (excluding amendments) must report on
the award most closely related to the proposal. The following
information must be provided:
- the NSF award number, amount and period of support;
- the title of the project;
- a summary of the results of the completed work, including
accomplishments, described in two separate sections, related to the
Intellectual Merit and Broader Impact activities supported by the award;
- publications resulting from the NSF award;
-- evidence of research products and their availability, including, but
not limited to: data, publications, samples, physical collections,
software, and models, as described in any Data Management Plan; and
-- if the proposal is for renewed support, a description of the relation
of the completed work to the proposed work."
* References Cited (II.C.2.e): "If there are no references cited, a
statement to that effect should be included in this section of the
proposal and uploaded into FastLane."
Thanks in advance for your attention to these new requirements.
----------------------------------------------------
From: yoram louzoun <louzouy@math.biu.ac.il>
Date: July 10, 2013 6:30:11 AM
Subject: Conference: PDEs and Dynamical..., Sep 30 - Oct 3, Bar Ilan U
Dynamics in biology conference - Sept. 30 2013 in Israel.
The PDEs and Dynamical Systems in Biology international conference will
take place from the 30th of Sept to the 3rd of Oct. at the Bar Ilan
University in Israel. The meeting is open for abstract and
mini-symposium submissions on all subjects related to dynamics in
biological systems. The abstract deadline is August 1st. There are no
registration fees, but we strongly encourage registration to asses the
number of participants.
The meeting website is: http://arielg333.wix.com/biu-pdebiology
Inquiries can be sent to: pdebiology@gmail.com or
Gil Ariel <arielg@math.biu.ac.il>
----------------------------------------------------
From: Marie-France Sagot <Marie-France.Sagot@inria.fr>
Date: July 17, 2013 8:03:34 AM
Subject: PhD Positions: Computational & Systems Biology, Lisbon & Lyon
In the context of a FP7 KBBE European Project, BacHBerry ("BACterial
Hosts for production of Bioactive phenolics from bERRY fruits"), we are
seeking two PhD candidates. The candidates will work:
- for one, in the CSI team at the IDMEC-IST in Lisbon, Portugal
(http://www.idmec.ist.utl.pt/);
- and for the other, in the BAMBOO team at the Inria-UCBL in Lyon,
France (http://team.inria.fr/bamboo/).
Both teams are methodological with an expertise in computational and
systems biology. Each successful candidate will also interact with the
team in the other country.
This project aims at tapping the potential of living organisms or
systems to develop or make natural chemical compounds that are believed
to be useful for medicine, agriculture, bioremediation, biodegradation,
or etc. Most often, the compound is already produced by the organism but
in small quantity, and one needs then to manipulate it in order for the
production to be increased. Other situations require transplanting part
of the chemical factory of an organism into another, in general a
bacterium, for better efficiency. In some cases, the transplant might
better be split among a community of different bacteria in interaction.
BacHBerry is more specifically interested in the generation of bacterial
platforms for sustainable bio-based production of phenolic compounds
found in berry fruits. Phenolics are recognised for their antioxydant
health-promoting and functional properties, and applied accross
applications as diverse as aromas, colours, nutraceuticals, and
medicines.
More specifically, we are looking for candidates with a Master in either
of the following areas: computer science, mathematics, statistics,
computational biology, metabolic engineering, regulation, or related,
with a strong taste for inter-disciplinary research, and with very good
interpersonal skills.
Ideally, the person will have some experience with optimisation
techniques and/or:
- for the group in Lisbon, in dynamic models, control theory or machine
learning;
- for the group in Lyon, in computational biology, graph algorithms or
statistics.
Both PhD students will be in co-supervision between the Portuguese and
French teams, with plenty of opportunities to travel between the two
countries.
Unsual CVs are welcome. Knowledge of the portuguese language
(Brazil / Portugal) would also be a plus :-)
Applications should include a motivation letter, a CV, copies of the
relevant certificates, and the address of three references. The
applications should be sent to both:
Susana Vinga, susanavinga@gmail.com
and
Marie-France Sagot, marie-france.sagot@inria.fr
ideally before August 15, 2013.
----------------------------------------------------
From: Hui, C. <chui@sun.ac.za>
Date: July 10, 2013 4:29:57 AM
Subject: Post-doc: Mathematical Ecology, Monash U, Australia
Research Fellow: Quantitative Ecologist / Mathematical Ecologist
A/Professor Melodie McGeoch is seeking an experienced Quantitative
Ecologist to explore the dynamics of biological communities,
specifically community responses to climate change and biological
invasion. This postdoctoral researcher will explore the theory of
community dynamics and responses to change using simulated and existing
empirical, spatially explicit plant community data. The research
outcomes will also be used to inform experimental and survey design of
ongoing, in-field data collection in collaboration with the research
group.
As the successful candidate, you will be expected to conduct theoretical
ecology research with a strong focus on spatially explicit population
and community dynamics. You will further be expected to maintain
consistently high research output in the form of quality publications,
supervise students, develop and submit grant proposals to external
funding agencies, contribute more generally to communicating the
research activities of the group, and participate in appropriate career
development activities.
Requirements
-A PhD in mathematical ecology, numerical ecology or community ecology
with a significant modelling component
-A publication track record in high-quality journals that clearly
reflects the ability to conduct publish research in the field of
numerical ecology
-Demonstrated evidence of a strong interest in both theoretical and
applied ecology, as well as population and community dynamics
-An excellent knowledge in the mathematical modelling of ecological
systems
-Demonstrated knowledge of data analysis in R and the use of Geographic
Information System software
-Strong statistical and mathematical skills, specifically mathematical
modelling, quantitative spatial analysis, spatial simulation and
randomization methods (analytical and numerical), Bayesian approaches
and general numerical methods in ecology
-Enthusiastic about collaborative research
-Have the ability to communicate effectively with other scientists at
the interface of empirical and theoretical ecology
-Have a strong command of English
Details see:
http://jobs.monash.edu.au/jobDetails.asp?sJobIDs=513717&lWorkTypeID=&lLocationID=&lCategoryID=641%2C+640%2C+636&lBrandID=&stp=AW&sLanguage=en
Interested applicants should contact Prof Melodie McGeoch:
melodie.mcgeoch@monash.edu
----------------------------------------------------
From: Asquith, Becca <b.asquith@imperial.ac.uk>
Date: July 10, 2013 6:19:43 AM
Subject: Post-doc: Theoretical Immunology, Imperial College London
Imperial College London
Immunology Section
Department of Medicine
Early Stage Research Fellow
Salary: 38,077.84 pounds per annum
An exciting opportunity has arisen for an Early Stage Research Fellow in
Theoretical Immunology in the Department of Immunology, at Imperial
College London.
You will join the Theoretical Immunology group headed by Dr Becca
Asquith, carrying out research on quantitative human T cell immunology.
You will have the opportunity to register for a PhD.
You must have a good first degree in an appropriate discipline (such as
Mathematics, Physics, Computer Science or Bioinformatics) or equivalent
qualifications or experience. An MSc in Mathematical Biology or
equivalent would be desirable. Previous experience of mathematical
immunology would be an advantage.
For informal enquires about the post please contact Becca Asquith
(b.asquith@imperial.ac.uk).
The post is full-time and fixed term for three years from September 2013
(start date negotiable), and is based at the St Mary's Campus,
Paddington, London.
Eligibility: The Marie Curie Initial Training Network is providing this
funding for an early stage researcher. This means a researcher who, at
the time of recruitment, has not yet been awarded a doctorate degree and
is in the first 4 years (full-time equivalent) of his/her research
career. At the time of recruitment the researcher must not have resided
or carried out his/her main activity (work, studies, etc) in the UK for
more than 12 months in the 3 years immediately prior to his/her
recruitment.
Our preferred method of application is online via our website at
http://www3.imperial.ac.uk/employment (please select "Job Search" then
enter the job title or vacancy reference number into ?Keywords?). Please
complete and upload an application form as directed quoting reference
number HM20132013157.
Alternatively, if you are unable to apply online, please email
hmrecr@imperial.ac.uk to request an application form.
Closing Date: 19 August 2013 (Midnight BST)
Imperial Managers lead by example:
http://www3.imperial.ac.uk/hr/procedures/support/opportunities/expectations
Committed to equality and valuing diversity. We are also an Athena SWAN
Silver Award winner, a Stonewall Diversity Champion and a Two Ticks
Employer.
----------------------------------------------------
From: Alan D. Rendall <rendall@uni-mainz.de>
Date: July 11, 2013 4:09:09 AM
Subject: Post-doc: Math with Applications in..., Johannes Gutenberg U
A position as postdoc (scientific assistant) in the group 'Applied
Analysis' at the Mathematics Department of the Johannes Gutenberg
University, Mainz, is available starting as soon as possible (payment
according to TV-L 13). It is initially for two years but an extension
may be possible.
The candidate is required to participate in teaching duties (in the area
of analysis) and to do research on mathematical problems which come from
applications in the natural sciences, particularly from biology.
Experience in mathematical biology is desirable but not essential.
The candidate must have a PhD in mathematics or a suitable related area.
For the teaching it is necessary to have sufficient knowledge of German
or to be prepared to acquire this knowledge before starting the
position.
The Johannes Gutenberg University is committed to increase the
proportion of women in scientific positions and therefore encourages
women to apply.
Handicapped applicants with suitable qualifications will be given
special consideration.
Please send applications by E-Mail to Anita Peffer-Kohl
(peffer-kohl@uni-mainz.de) with CV, publication list, research plan and
names of two referees. Deadline 16.8.2013.
For legal purposes the German version of this advertisement is the
official one. It can be reached via the web page
http://www.mathematik.uni-mainz.de/arbeitsgruppen/angewandte-analysis
where further information about the group is also available.
----------------------------------------------------
From: Marie-France Sagot <Marie-France.Sagot@inria.fr>
Date: July 17, 2013 8:02:51 AM
Subject: Post-docs: Computational & Systems Biology, Lisbon & Lyon
In the context of a FP7 KBBE European Project, BacHBerry ("BACterial
Hosts for production of Bioactive phenolics from bERRY fruits"), we are
seeking two postdoc candidates, each for one year, possibly renewable
for up to three years. The candidates will work:
- for one, in the CSI team at the IDMEC-IST in Lisbon, Portugal
(http://www.idmec.ist.utl.pt/);
- and for the other, in the BAMBOO team at the Inria-UCBL in Lyon,
France http://team.inria.fr/bamboo/).
Both teams are methodological with an expertise in computational and
systems biology. Each successful candidate will also interact with the
team in the other country.
This project aims at tapping the potential of living organisms or
systems to develop or make natural chemical compounds that are believed
to be useful for medicine, agriculture, bioremediation, biodegradation,
or etc. Most often, the compound is already produced by the organism but
in small quantity, and one needs then to manipulate it in order for the
production to be increased. Other situations require transplanting part
of the chemical factory of an organism into another, in general a
bacterium, for better efficiency. In some cases, the transplant might
better be split among a community of different bacteria in interaction.
BacHBerry is more specifically interested in the generation of bacterial
platforms for sustainable bio-based production of phenolic compounds
found in berry fruits. Phenolics are recognised for their antioxydant
health-promoting and functional properties, and applied accross
applications as diverse as aromas, colours, nutraceuticals, and
medicines.
More specifically, we are looking for candidates with a PhD in either of
the following areas: computer science, mathematics, statistics,
computational biology, metabolic engineering, regulation, or related,
with a strong taste for inter-disciplinary research, and with very good
interpersonal skills.
Ideally, the person will have a long experience with optimisation
techniques and:
- for the group in Lisbon, in dynamic models and control theory;
- for the group in Lyon, in graph algorithms and discrete
combinatorics.
Unsual CVs are welcome. Knowledge of the portuguese language
(Brazil / Portugal) would also be a plus :-)
Applications should include a motivation letter, a CV, and the address
of three references. The applications should be sent to both:
Susana Vinga, susanavinga@gmail.com
and
Marie-France Sagot, marie-france.sagot@inria.fr
ideally before September 15, 2013.
----------------------------------------------------
From: Christine Kelly <ckelly@co57.com>
Date: July 17, 2013 9:28:10 AM
Subject: Job Openings: Co57 Systems, Cambridge, MA
Co57 Systems
Building Visual Intelligence
Co57 designs cognitive architectures for artificial vision systems,
enabling them to perceive and interact with the world.
Research and Development - Open Positions:
http://co57.com/jobs.html
Job Description-
Located in Cambridge, MA.
Research and development of a real-time robot vision system for
detection of objects, actions, and events.
Responsibilities:
-Developing computational models of activity recognition, scene
understanding, and motion analysis
-Building a real-time vision system out of distributed, asynchronous
components
-Demonstrating working solutions with quantifiable results.
-Taking ownership of topics, periodically writing and presenting
internal reports.
We have several types of positions available, depending on experience:
[1] Research Associate
This is a temporary position, anywhere from 3-6 months, typically for
summer interns.
-B.S or M.S in
Computer Science / Computational Neuroscience / Math / Physics
-Passion for building real-time vision systems.
-Excellent coding skills in C++ and Python.
-Experience with development on Linux platforms
-Good interpersonal skills and ability to work well as part of a team.
Please send resumes to jobs@co57.com with the subject
"Research Associate."
[2] Research Engineer
-B.S. or M.S. in Computer Science or Computational Neuroscience
-Passion for designing fast, real-time algorithms
-Excellent coding skills in C++ and Python.
-Knowledge of Statistical and Machine learning techniques
-Total familiarity with Linux, and development on Linux platforms
(e.g. g++, gdb, emacs/vi)
-Good interpersonal skills and ability to work well as part of a team.
Please send resumes to jobs@co57.com with the subject
"Research Engineer."
[3] Systems Engineer
-B.S. or M.S. in Computer Science
-Extensive experience in building and maintaining software/hardware
infrastructure (including essential functions like networking, data
security and backup)
-Excellent coding skills in C++ and Python.
-Experience with implementing software architectures for real-time
performance, especially shared/distributed memory, and IPC paradigms
-Total familiarity with Linux, and development on Linux platforms
(e.g. g++, gdb, emacs/vi)
-Good interpersonal skills and ability to work well as part of a team.
Please send resumes to jobs@co57.com with the subject
"Systems Engineer."
[4] Development Scientist
-Ph.D in Computer Science or Computational Neuroscience with a strong
background in human visual perception, and computer vision.
-Prior experience in building vision systems.
-Extensive knowledge of the state-of-the-art Statistical and Machine
learning techniques - and the creativity to realize their limitations.
-Excellent coding skills in C++ and Python.
-Experience with development on Linux platforms
-Strong mathematical ability.
-Good interpersonal skills and ability to work well as part of a team.
Please send resumes to jobs@co57.com with the subject
"Development Scientist."
----------------------------------------------------
From: Linda Petzold <petzold@cs.ucsb.edu>
Date: July 16, 2013 6:09:52 PM
Subject: First Release of StochSS: Stochastic Simulation Service
We are excited to announce the first release of StochSS: Stochastic
Simulation Service. StochSS is an integrated development environment
featuring state of the art algorithms for discrete stochastic
biochemical simulation. StochSS is designed to enable you to easily
scale up your simulations in complexity, deploying compute resources as
needed. The current version includes algorithms for simulation of
well-mixed systems. Problems can be specified via a graphical user
interface (or imported as StochKit2 models).
For more details and instructions on how to obtain the code, visit us at
www.StochSS.org.
----------------------------------------------------
Subject: SMBnet Reminders
To subscribe to the SMB Digest please point your browser at
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The SMB Digest is also available on the SMB Home Page at
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The contents of this publication may be reproduced in whole or in part
with attribution.
End of SMB Digest
****************************************************