| News & Commentary |
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The newsletter includes some of the best of our various online forums and details some of our internal (and external) activities.
IN THIS ISSUE:
- Bioinformatics to Systems Biology 2008 wrap-up
- Poll: Next language
- Project spotlight: CD-HIT
- Career Center job search
- Upcoming events
URL: [link]
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LOCALE: Toronto, ON, Canada
DATES: October 3-4, 2008
COURSE OUTLINE:
Extracting true, meaningful information from a data set with enough confidence to guide future research projects involves a solid understanding of statistics. The CBW Faculty has developed a 2-day intensive course covering all of the essential topics in statistics needed to improve your understanding and use of statistics in your research. Using common research scenarios such as microarray data, flow cytometry and SNP data, participants will gain practical skills and understanding on the essential statistics in biology.
Each module contains approximately 1.5 hours lecture, 30 minute break and a lab.
DAY 1: Modules: (1) Exploratory data analysis and common statistical assumptions in biology, (2) Hypothesis testing, (3) Multivariate analysis, and (4) Bayesian vs. Frequentist
DAY 2: Modules: (5) Linear Regression Modeling Strategies, (6) Binary logistic regression, (7) Survival analysis models, and (8) Statistics for Genome-wide Association Studies
LEAD FACULTY (2008): Raphael Gottardo & Laurent Briollais
REGISTRATION FEE: $750 + GST
Register now as space is limited to 30 participants. A comprehensive lecture and laboratory manual will be provided.
FOR MORE INFORMATION:
Full details and application forms: [link]
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The next distance courses in Bioinformatics from the University of Manchester and the University of Leeds, UK, begin on 6 October 2008. The payment deadline is Friday 19 September.
These Masters level courses follow two themes, Bioinformatics and Computer Science. The Bioinformatics courses are:
- Introduction to Molecular Biology for Computer Scientists
- Introduction to Bioinformatics
- Bioinformatics for Systems Biology
- Introduction to Microarray Data Analysis
- Theory and Applications in Bioinformatics
- The Bioinformatics of Protein Structure
- The Science of Proteomics
- Molecular Modelling and Structure-based Drug Design
The computing courses are:
- Introduction to software development in Java
- Intermediate Java
- Biocomputing
- Object-oriented analysis and design with UML
- Introduction to Ontologies for the Biosciences
FOR MORE INFORMATION:
You will find further information, including fees and a link to the online application form, here: [link]. If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk
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After three years of hard work, we are happy to announce the first specification for Process Diagrams of the Systems Biology Graphical Notation!
The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual representation of essential biochemical and cellular processes studied in Systems Biology. SBGN defines a comprehensive though limited set of symbols with precise semantics, together with detailed syntactic rules defining their use. It also describes the manner in which such graphical information should be interpreted.
Standardizing graphical notations for describing biological interactions is an important step towards the efficient and accurate transmission of biological knowledge between different communities. Traditionally, diagrams representing interactions among genes and molecules have been drawn in an informal manner, using simple unconstrained shapes and edges such as arrows. Until the development of SBGN, no standard agreed-upon convention existed defining exactly how to draw such diagrams in a way that helps readers interpret them consistently, correctly, and unambiguously. By standardizing the visual notation, SBGN can serve as a bridge between different communities such as computational and experimental biologists, and even more broadly in education, publishing, and more.
SBGN is formed of three languages offering different views of a biological system. The present specification defines the Level 1 of the Process Diagram notation, aimed to describe the causal sequences of molecular processes and their results. It is the result of numerous discussions and exchanges, between many individual and groups, and is very much a community work. The result should hopefully suits the result of most users while being unambiguous.
FOR MORE INFORMATION:
More information on SBGN and SBGN Process Diagram Level 1 can be found at http://www.sbgn.org/ and through the mailing-list sbgn-discuss@sbgn.org
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Bioinformatics.Org is now offering Perl and MySQL training as "Bioinformatics Programming" courses. The first in this series is the introductory level course, CS101A Introduction to Bioinformatics Programming, to be held September 15-19, 2008, 15:30-17:30 GMT daily (this is a combination of our previous Perl and MySQL Level 1 courses).
OBJECTIVE:
This course teaches biologists how to use programming as a way to automate biological data analysis and develop algorithms or workflows, and how to manage vast amounts of data using database technologies. Data could be DNA or Amino Acid sequences, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. Perl for programming and MySQL for database management will be covered.
SYLLABUS:
The course is divided into 8 sessions, roughly 1-1.5 hours each, and 2 sessions are held every day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.
- Session 1 will cover fundamentals of databases and deciding what to store, and how to install a database.
- Session 2 will cover database concepts such as creating and designing a database, and populating the database with sample data.
- Session 3 will cover data retrieval and manipulation concepts using SQL queries (Select, Update, Delete, Insert).
- Session 4 will cover additional topics like interfacing the database with the Microsoft Access front end, and mining the data using the Perl database interface.
- Session 5 will cover installation issues and simple exercise that illustrate how to create and execute simple Perl programs. The Perl environment will be introduced.
- Session 6 will cover fundamentals of programming with Perl, such as scalars, arrays, variable interpolation, operators (mathematics, conditional, logical), file input/output, printing, loops (if-then-else, for, while), list operations, etc.
- Session 7 will cover functions/ subroutines, hash arrays and regular expressions.
- Session 8 will cover the installation of Perl packages, and some examples of using the famous package BioPerl, for manipulating sequences, automating BLAST queries, etc. A project will be assigned.
FOR MORE INFORMATION:
[link]
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Call for Participation: ACM Second International Workshop on Data and Text Mining in Bioinformatics (DTMBIO 2008) in conjunction with ACM 17th CIKM 2008
LOCALE: Napa Valley, California
DATE: October 30, 2008
Early registration deadline for the workshop is August 22, 2008.
Information on Two keynote speakers (Dr. Russ Altman and Dr. Alfonso Valencia) is available at [link]
The list of accepted papers (regular and short) is up on the website, where you can register online.
FOR MORE INFORMATION:
The papers are made available at [link]
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A new issue of EMBnet.news is out. Among the contents:
- New tools for bioinformatics teaching.
- ChemGPS-NPweb- a tool for navigation in biological relevant chemical space,
- The GRID in practice,
- LUPA: "Unravelling the molecular basis of common complex human disorders using the dog as a model system"
and much more.
EMBnet.News can be downloaded for free at http://www.embnet.org or direct link for printing: [link]
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LOCALE: Georgian Terrace Hotel, Atlanta, GA
DATES: October 18-21, 2008
International Launch Conference
Introducing the New Integrative BioSystems Institute at the Georgia Insitute of Technology
With this conference, the Georgia Institute of Technology announces and celebrates the launch of its new Integrative BioSystems Institute (IBSI). Frontiers in Multi-Scale Systems Biology will highlight representative topics of multi-scale systems biology including: genomics; proteomics; metabolomics; molecular inventories and databases; modeling and simulation; high-performance computing; enabling experimental and computational technologies; as well as applications in cancer, neuroscience and the environment. The conference will feature invited speakers and contributed poster presentations.
The conference banquet will be held in the Oceans Ballroom of the Georgia Aquarium, the largest aquarium in the world. During dinner, guest can view beluga whales and various fishes through two large aquatic observation windows.
FOR MORE INFORMATION:
For more information and registration, please visit: http://www.ibsi.gatech.edu/frontiers
Contact Information:
Ms. LaDawn Terry
Georgia Institute of Technology
313 Ferst Drive
Atlanta, GA 30332-0535
contact@ibsi.gatech.edu
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We at Ocimum Biosolutions, take pride in announcing the inception of the Genomic Pioneers Award, a tribute towards acclaiming the immense efforts and perseverance of researchers involved in life science research.
At Ocimum Biosolutions, we understand the value of patience and perseverance that goes into setting new heights in research which is why the Genomic Pioneers Award would stand as a token of appreciation towards recognizing the outstanding contribution of researchers to the field of Genomics working with state-of-the-art techniques.
The first issue of Genomic Pioneers Award would be presented to innovations in Oligonucletide Application Techniques which have significant impact on the advancing Genomics research.
The award, which will include a cash prize of € 3000 (100,000 INR), would be presented to researchers (senior or early-career investigators) from academic or private sectors, who have demonstrated innovative excellence in the use of oligonucleotides based techniques in the area of Genomics. The award is being constituted in the month of October (Europe) and September (India) 2008.
Application forms are available online. Just fill it out and mail it to us on or before 20th September 2008 for Europe and 30th August 2008 for India.
FOR MORE INFORMATION:
To learn more about the Genomic Pioneers Award, please visit: [link]
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Manchester Informatics (http://www.informatics.manchester.ac.uk/) is delighted to be able to announce the award of funding to develop two new courses in Systems Biology. These new courses will follow from our existing online course, Bioinformatics for Systems Biology.
Bioinformatics for Systems Biology enables the successful student to: explain the need for models of systems; understand network layouts, using Cytoscape; understand the use of protein-protein interaction networks in function prediction.
The final section of this course introduces dynamic models. The details are available here: [link]
The two new courses will be:
1. Mathematics for metabolic modelling
2. Computational simulation and analysis of biochemical networks
'Mathematics for metabolic modelling' will provide the necessary mathematical background for the second course, 'Computational simulation and analysis of biochemical networks'. The software used will include Cytoscape, CellDesigner and COPASI.
FOR MORE INFORMATION:
For further information, please contact Heather.Vincent@manchester.ac.uk
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| Acknowledgments |
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We wish to thank the following for their support:
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