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Monday, March 28, 2011

Intech Launches Open Access Journal "Nanomaterials and Nanotechnology"

InTech, the Open Access publisher, has announced the launch of a new Open Access journal, "Nanomaterials and Nanotechnology". The quarterly journal will be available online for free full-text download on the reading platform www.InTechOpen.com.

Open Access publications which are not subsidized by institutional funding are usually financed by payments met by the institutions researchers work for. However, "Nanomaterials and Nanotechnology" will be a "Free for All" publication, with no costs incurred by contributors or readers.

Thanks to the "one at a time" publishing model, accepted papers will be published online immediately following peer review. The complete process from submission to publication will take approximately one month.

The journal's Editor in Chief is Dr. Paola Prete of the Institute for Microelectronics and Microsystems at the Italian National Research Council, Lecce, Italy. Dr. Prete expects that the journal will be a useful source of information for researchers in all areas of nanoscience since it will cover a wide range of topics, such as the synthesis of nanosized materials, nano-characterization techniques, nanobiotechnology and nanomedicine.

The Editorial Board is comprised of international experts, including C. N. R. Rao - Linus Pauling Research Professor at the Jawaharlal Nehru Centre for Advanced Scientific Research and Honorary Professor at the Indian Institute of Science, Bangalore, India. Professor Rao is a member of the Royal Society and the US National Academy of Sciences, and is renowned for his contribution to solid state chemistry and nanomaterials over the last two decades.

The first issue of the Journal is expected to go live in June 2011. The call for papers for inclusion in the first issue is open until 10 May, 2011.

Researchers interested in submitting their papers for consideration for the first issue are invited to find out more at http://www.intechweb.org/nn-first-issue.html.


InTech (www.intechweb.org) is an Open Access publisher of journals and books covering the fields of Science, Technology and Medicine. InTechOpen is an Open Access reading platform for InTech publications, a space where all users can read, share and download more than 300 books and 8,000 book chapters. All content at InTechOpen (www.intechopen.com) is distributed under the Open Access label and under the Creative Commons license - freely accessible to anyone, anywhere in the world.

URL: http://www.intechweb.org

Contact Person: Nataly Anderson (anderson@intechweb.org)

Sunday, March 27, 2011

Announcing RECOMB-BE 2011 in Vienna, Austria, July 20-21, 2011

Third RECOMB Satellite Conference on Bioinformatics Education
Vienna, Austria
July 20-21, 2011
in Conjunction with ISMB 2011


The Third Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE) will be held in Vienna, Austria, July 20-21, 2011 as an ISMB/ECCB 2011 Satellite Meeting (http://www.iscb.org/ismbeccb2011). The conference follows the first two RECOMB-BE meetings: http://casb.ucsd.edu/bioed/ and http://casb.calit2.net/bioed10/ . RECOMB-BE 2011 will consist of invited presentations, oral presentations selected from submitted abstracts and papers, a poster session, and discussion panels, all of which focus on improving bioinformatics education.


Partial List: Laurie Heyer (Davidson College), Larry Hunter (University of Colorado), Fran Lewitter (Whitehead Institute for Biomedical Research) Ran Libeskind-Hadas (Harvey Mudd College), Florian Markovetz (CRUK Cambridge Research Institute), Bernard Moret (École Polytechnique Fédérale de Lausanne), Tal Pupko (Tel Aviv University), Pavel Pevzner (University of California at San Diego), Ben Raphael (Brown University), Ron Shamir (Tel Aviv University), Beth Simon (University of California at San Diego), Terry Speed (University of California at Berkeley), and Jens Stoye (Bielefeld University).


The goal of RECOMB-BE is threefold: to showcase best practices of teaching bioinformatics ideas to biology undergraduates, to discuss existing challenges in bioinformatics education (with an emphasis on undergraduate education), and to promote collaboration among educators with the aim to develop a mature bioinformatics curriculum. In keeping with the focus on undergraduates, the conference will also showcase selected bioinformatics research projects conducted by undergraduate students.

While biology has been transformed into a computational science in the last decade, the biological curriculum remains largely unchanged with respect to computational issues. The question: "How should we teach bioinformatics to biology students?" has become of the utmost importance, since many universities have not only founded undergraduate bioinformatics programs but are considering the addition of new computational courses to the standard biology curriculum—a change which would represent a dramatic paradigm shift in biology education. However, as the first two RECOMB-BE meetings demonstrated, there is a great divide in how even the world's top bioinformaticians thought the subject should be taught, and therefore the above pedagogical question has not been answered satisfactorily to date.

RECOMB-BE therefore aims to demonstrate the intricacy, practicality, and beauty of modern bioinformatics at the undergraduate level, and advance the discussion about its curriculum in the biology classroom. For a summary of RECOMB-BE discussions and the educational challenges that lie ahead for bioinformatics, see Computing has changed biology--biology education must catch up (Science 2009, v.325: 541-542).


RECOMB-BE will have a somewhat unusual format, inspired by the biennial mathematical conference called Gathering for Gardner (G4G) At G4G, leading mathematicians give high-school and undergraduate level lectures; the goal of G4G is therefore to present complex mathematical ideas in a simple form. This objective is one for which the bioinformatics community must also strive in order to establish meaningful future collaborations with biologists and to bridge the cultural gap between computational and experimental scientists.

Unlike previous meetings on bioinformatics education, which have focused on how bioinformatics should be taught, RECOMB-BE showcases how leading bioinformaticians actually teach. Speakers will give short, introductory-level lectures, aimed at undergraduates. These lectures will be complemented by discussion panels focusing on existing challenges in bioinformatics education as well as poster presentations given by undergraduate students on their research projects.


The participants of RECOMB-BE in 2009 and 2010 formed the Bioinformatics Education Alliance, a group of sixteen leading bioinformaticians who have recently collaborated to produce a textbook, called Bioinformatics for Biologists (B4B). The first edition of B4B will be published by Cambridge University Press in the summer of 2011, and test copies will be available at ISMB 2011. Please see the official B4B website for more details: http://cseweb.ucsd.edu/~ppevzner/B4B/

B4B is an open project that will be continuously expanded by new chapters. Therefore, RECOMB-BE invites submissions of proposals for new chapters; accepted chapters will be included in the second edition of B4B which is scheduled for publication in 2012 (see "Important Dates" below).


We invite submissions in four categories:

1. Bioinformatics Education Papers
2. Bioinformatics for Biologists Textbook Chapter Proposals
3. Bioinformatics Education Abstracts (submitted by educators)
4. Undergraduate Bioinformatics Research Abstracts (submitted by undergraduate or first-year graduate students)

Selected papers and abstracts in the first three categories will be invited for either oral or poster presentations. Undergraduate bioinformatics research abstracts will be invited for a poster presentation.

Bioinformatics Education Papers should be submitted via the RECOMB-BE website and must be received by May 5, 2010. Each paper should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Papers should be self-contained and aimed at advanced undergraduate biology students. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. RECOMB-BE imposes no explicit restrictions on format, length, or notation, as we encourage contributors to choose the style they feel is the most appropriate; however, we anticipate that each contributed paper will be at least 10 pages long.

Authors of selected papers will be invited to submit their paper in the journal PLOS Computational Biology (in the Education Article category) as well as a chapter in the second edition of the Bioinformatics for Biologists textbook, which is described above.

Bioinformatics for Biologists (B4B) Chapter Proposals should be submitted via the RECOMB-BE website and must be received by May 15, 2011. Each submission in this category should constitute a brief description of the proposed chapter. Authors of selected proposals will be invited either for oral or poster presentations at RECOMB-BE 2011. In addition, these authors will be asked to submit a full-length chapter for the second edition of B4B shortly after RECOMB-BE. Proposals should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. We anticipate that each chapter proposal will be 1-2 pages long.

Bioinformatics Education Abstracts (submitted by educators) should be submitted via the RECOMB-BE web site and must be received by May 20, 2011. Submissions in this category can discuss practice, challenges, or perspectives in bioinformatics education (e.g., curricula, integration of bioinformatics programs, online courses, etc.) or represent a proposal for a short 20-30 minute introductory lecture aimed at undergraduates. We are specifically looking for lectures that begin with a description of an interesting biological problem, such as "Did we evolve from Neanderthals?" and then show how computational techniques can be used to solve this biological problem. Each abstract should be at most 1 page long.

Undergraduate Bioinformatics Research Abstracts (submitted by undergraduates or first-year graduate students reporting their undergraduate work) should be submitted via the RECOMB-BE website and must be received by May 20, 2011. Each abstract should be at most 1 page long.


RECOMB-BE and the Howard Hughes Medical Institute offer travel support to undergraduate students interested in bioinformatics. All undergraduate students are invited to apply for travel support. RECOMB-BE will have a poster session showcasing undergraduate bioinformatics research, and we encourage undergraduate students interested in participation to submit an undergraduate bioinformatics research abstract. Students who submit abstracts will be given a priority with regards to travel support. First-year graduate students who wish to present their undergraduate work are also welcome to apply for travel support. All applications for travel support should be made via RECOMB-BE website.

In addition to supporting undergraduate students, RECOMB-BE also has limited funds to support authors of accepted RECOMB-BE papers and B4B chapter proposals.


Paper submission deadline: May 5, 2011
Notification of paper acceptance: May 15, 2011
Bioinformatics for Biologists textbook chapter proposals deadline: May 15, 2011
Notification of proposal acceptance: May 25, 2011
Abstract submission deadline: May 20, 2011
Notification of abstract acceptance: May 25, 2011
Application for travel support deadline: June 5, 2011
Notification of travel support: June 15, 2011


RECOMB-BE was founded by Pavel Pevzner (UCSD) and Ron Shamir (Tel Aviv University) in 2009.

RECOMB-BE 2011 Program Committee: Fran Lewitter (Whitehead Institute for Biomedical Research), Ran Libeskind-Hadas (Harvey Mudd College), Pavel Pevzner, (UCSD) and Ron Shamir (Tel Aviv University).

RECOMB-BE Organizing Committee: Phillip Compeau (Chair), Sangtae Kim, and Son Pham.

Email contact: pcompeau@math.ucsd.edu


RECOMB-BE is supported by the Howard Hughes Medical Institute (HHMI), the International Society for Computational Biology (ISCB), and the California Institute for Telecommunications and Information Technologies (CalIT2).


The RECOMB International Conference on Research in Computational Molecular Biology was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference arose from the need to advance research on the mathematical and computational side of molecular biology, and today the conference maintains its focus on state-of-the-art computational advances in this field. The 15th Annual RECOMB conference (RECOMB 2011) will be held March 28-31, 2011 in Vancouver, Canada. The conference website can be found at http://compbio.cs.sfu.ca/recomb2011/.

The RECOMB Satellites Series was founded by Pavel Pevzner in 2001. It contains today nine focused meetings covering various specialized aspects of bioinformatics: RECOMB Comparative Genomics, RECOMB Regulatory Genomics, RECOMB Computational Cancer Biology, RECOMB Computational Proteomics, RECOMB SNPs and Haplotypes RECOMB Systems Biology, RECOMB Massively Parallel Sequencing and of course RECOMB Bioinformatics Education.
URL: http://casb.ucsd.edu/bioed11/index.php

Contact Person: Phillip Compeau, University of California-San Diego Dept. of Mathematics (pcompeau@math.ucsd.edu)

Thursday, March 17, 2011

NEW NSF Solicitation: AVAToL

AVAToL, Assembling, Visualizing and Analyzing the Tree of Life

The Assembling, Visualizing and Analyzing the Tree of Life (AVAToL) activity supports novel and transformative approaches to the development of an integrated and robust tree of life, as well as visualization and analysis on a dynamic tree of life. This will take place through the Ideas Lab project development and review process. The goal of this activity is to identify opportunities for investment to significantly advance the state-of-the-art in tree construction, visualization, and analysis across the tree of life. Participants selected through an open application process will engage in an intensive five-day residential workshop to generate project ideas through an innovative, real-time review process. New multidisciplinary teams will form during this workshop to engage in creative problem solving directed at outstanding problems concerning the tree of life. Multidisciplinary integrative approaches calling for communication and interaction among diverse scientists are key to the success of the approach. For example, in addition to those working in systematics and phylogenetics, AVAToL might benefit from mathematicians and computer scientists to contribute algorithms and models, bioinformaticians or genomicists to contribute data pipelines and novel molecular characters, or statisticians and artists with an interest in novel methods of visualization and interactive use of the tree of life. Therefore, members of the systematics research community, bioinformaticians, genomicists, morphologists, paleontologists, computer scientists, statisticians, mathematicians, educators involved in training the next generation of researchers, and representatives of any other disciplines that might contribute important ideas are all strongly encouraged to apply.
URL: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503629&org=BIO&from=home

Contact Person: Tim Collins (bio-AVAToL@NSF.gov)

Thursday, March 10, 2011

SIB Swiss Institute of Bioinformatics Awards 2011-Call for Applications

The SIB Swiss Institute of Bioinformatics is happy to announce the SIB 2011 Awards, two prizes assigned to young scientists in bioinformatics.
Two categories: SIB Young Bioinformatician Award and SIB Best Graduate Paper Award.

SIB 2011 Young Bioinformatician Award

Prize of CHF 10,000 and award certificate.

Open to any graduate student or young researcher in Europe who has carried out a research project centered on the in silico analysis of biological sequences, structures and processes.
Candidate must not be more than 32 years old at the time of submission and must have worked on a project with a partner in Switzerland for at least 6 months in 2010.

Submitted project must be completed or subject to publication within the period from 1 June 2010 to 1 June 2011.

Applications for the award may be submitted by the candidate, any faculty member or SIB group leader.

SIB 2011 Best Graduate Paper Award

Prize of CHF 5,000 and award certificate.

Open to any graduate student who has not yet completed his/her PhD, at the time the paper was published.

Applicant must have studied in Switzerland for at least 6 months in 2010.
Submitted paper must have been published or be subject to publication within the period from June 1, 2010 to June 1, 2011.

Applications for the award may be submitted by the candidate, by any SIB group leader or by a Swiss university or federal institute of technology.

Both winners will receive their prizes during the [BC]2
Basel Computational Biology Conference on 23-24 June 2011.
Winners will also be invited to present their projects during the conference.

Closing date for entries: 30 March 2011

More information and submission form at:

Irene Perovsek
00 41 (0)21 692 40 54
URL: http://www.isb-sib.ch/research/sib-awards.html)