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eyeLIMS is a community-driven project which aims at providing a Free Open Source Laboratory Information Management System (LIMS) powered by the web operating system eyeOS (http://www.eyeos.org/).
eyeOS provides both a secured web-based desktop-like environment and a set of libraries for easy development of web applications. It is mainly coded in PHP, XML and javascript but other languages (MySQL, Python, Flash, Java...) can be easily integrated.
The eyeLIMS community will develop new eyeOS applications or port to eyeOS existing free open source applications specifically dedicated to molecular and cellular biology.
The eyeLIMS Software Suite will include a set of eyeOS applications dedicated to common activities in research laboratories such as managing samples or reagents (eyeStorage), managing bibliographic references (eyeBiblio) or manipulating data (eyeJmol).
The whole project is Free and Open Source and will be released under GNU Affero GPL v.3 license.
eyeLIMS is a community-based project so feel free to join us!
FOR MORE INFORMATION:
You can discover and join the project at: http://www.eyelims.com/
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ISCB-RSG (Regional Student Group)-India and ISCB-RSG-Korea are collaborating to provide a rare opportunity to undergraduate students by initiating a joint project on "Dynamic or Evolutionary co-expression network on yeast cell cycle".
The purpose of this investigation is based on understanding biological dynamics behavior of gene-gene interaction during cell cycle. The project involves collaboration with Computational Biology Research Center, AIST, Japan and KOBIC (Korea Bioinformatics Center), Korea.
REQUIREMENTS:
The student is an Indian national studying in any accrediated university, plus
- Molecular biology, background in math, physics, and biochemistry.
- Programming: Perl, C or R (not recommend).
- Good Internet connection during the course of the project
DURATION: 3 MONTHS
Don’t miss this excellent opportunity to extend your knowledge in computational biology, to practical applications, by working with highly experienced scientists and research fellows. It is a chance to get valuable live hands on experience on a project which will help you understand the essence of research in bioinformatics.
DEADLINE: 17th May, 2008
Submit your application by sending an email to rsg-india@iscbsc.org with a brief paragraph stating why you should be selected to work on this virtual project and what are you looking in terms of knowledge gain from this project. Also attach a copy of your CV. Please keep the subject line as RSG-KICP Application. Successful candidates will be informed by 26th May 2008.
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LOCALE: Simon Fraser University, Burnaby, BC, Canada
DATES: July 24-30, 2008
The ACGC introduces biologists to some of the latest methods in bioinformatics, including DNA and protein sequence analysis, automation of data analysis, web services and workflows, and high-throughput genome annotation. The course is led by researchers from the Genome Canada Bioinformatics Platform. Both lectures and extensive hands-on tutorial sessions are included.
The project is supported by Genome Alberta and Genome Canada, a not-for-profit organization which is leading Canada's national strategy on genomics with $600 million in funding from the federal government.
FOR MORE INFORMATION:
http://www.gcbioinformatics.ca/training
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LOCALE: The National eScience Centre, Edinburgh, Scotland
DATES: May 21-22, 2008
This two-day introductory ‘hands-on’ workshop aims to provide attendees with both the theoretical foundations and practical experience to begin building OWL ontologies using the latest version of the Protégé-OWL tools (Protege4). It is based on Manchester's well-known "Pizza tutorial" (see http://www.co-ode.org).
This tutorial will cover the main conceptual parts of OWL through the hands-on building of an ontology of pizzas and their ingredients. A series of exercises take attendees through the process of conceptualizing the toppings found on a pizza; the entry of this classification into the Protégé environment; the description of many types of pizza. All this is set in the context of using automatic reasoning to check the consistency of the growing ontology and to use the reasoner to make queries about pizzas. Since 2003 this tutorial, in various forms, has been given over 20 times and been attended by hundreds of budding ontologists.
AIMS:
The aims of this tutorial are to:
- understand the use of ontologies
- understand statements written in OWL;
- understand the role of automatic reasoning in ontology building;
- build an ontology and use a reasoner to draw inferences based on that ontology;
- gain experience in the Protégé 4 ontology building environment;
- gain insight into how OWL can play a role in semantic metadata.
FOR MORE INFORMATION:
http://www.nesc.ac.uk/esi/events/895/
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Master of Science Degree in Biochemistry and Molecular Biology - Bioinformatics Track at Georgetown University Medical Center, Washington D.C.
This one-year M.S. degree program has an interdisciplinary curriculum covering both biomedical and computational sciences. Built upon the unique research strengths and bioinformatics infrastructure at the Protein Information Resource (PIR) and Georgetown University, the curriculum emphasizes bioinformatics of genomics, proteomics and systems biology. With computer-lab based courses and a 16-week bioinformatics internship, students will gain hands-on experience in applying bioinformatics as an integral approach to biomedical research, from basic molecular sequence analysis to advanced high-throughput omics data analysis.
Bioinformatics is fundamental to the modern day study of biology and is essential to 21st century biomedical research. This program is designed for students who would like to gain knowledge and experience in both Biochemistry/Molecular Biology and Bioinformatics. With bioscience and computing skills, the graduates are equipped to play a key role in interdisciplinary and multidisciplinary teams. Graduates may pursue further study towards a PhD, MD, MBA or law degree or pursue a career in industry, government or academia as a bioinformatics professional.
FOR MORE INFORMATION:
See [link] or contact Dr. Cathy Wu (bioinformatics@georgetown.edu).
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LOCALE: University of Maryland (US)
DATES: The following courses are scheduled:
- May 13-14, 2008
- Sept. 9-10, 2008
- Nov. 5-6, 2008
The Institute for Genome Sciences at the University of Maryland School of Medicine is offering a free prokaryotic genome annotation workshop for those interested in training in genomics. Each session is 2 days long and there are three sessions scheduled for this year.
Day 1 includes instruction on all elements of the IGS prokaryotic annotation pipeline including:
- Gene finding
- Similarity searching
- Gene model curation
- Evidence evaluation for protein functional annotation
- The Gene Ontology system
- Data storage in a relational database
- The Annotation Engine Service
Day 2 focuses on the use of the Manatee manual annotation tool. The day begins with a detailed demonstration of the features available within Manatee. This is followed by instructor led group annotation of several proteins. Finally, attendees engage in hands-on exercises where they annotate several proteins on their own. The instructor then annotates these proteins with the whole group so that attendees can review the annotations they made.
Computers are provided for use during the workshop. In addition, all attendees will receive a CD containing workshop presentations, tutorials, and supplementary materials.
There are only 25 spots available for each session, so register soon if you'd like to attend.
FOR MORE INFORMATION:
[link]
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LOCALE: Boston, MA (US)
DATES: April 28-30, 2008
Bioinformatics.Org will once again hold its Annual Meeting at the Bio-IT World Conference & Expo in Boston, Massachusetts, and we thank the fine folks at Cambridge Healthtech Institute for providing this venue to us.
Here's a look at our schedule for next week:
Monday, April 28: We'll be in booth #102 for the opening of the exhibit hall, 5:00-7:00 PM.
Tuesday, April 29: The 2008 Benjamin Franklin Award will be given to Robert Gentlemen at 9:00 AM, and he will give the laureate seminar until 9:30 or so. Afterward, we'll be at the booth for the rest of the day. If I'm not there, you might find Shailender Nagpal, who is our instructor for scripting language, microarray analysis and database courses.
Wednesday, April 30: We'll be at the booth again from 9:45 AM to 2:00 PM.
We'll be sure to put some photos from the event in the May issue of the newsletter. We should also have some announcements to make at the event!
Bio-IT World has a $50 exhibit hall pass, which will also get you into the Franklin Award ceremony and the other keynotes. The full program is worthwhile as well. I've been attending each year since the start, and the conference has been getting quite large, attracting many more attendees in recent years.
FOR MORE INFORMATION:
http://bio-itworldexpo.com/
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The Department of Bioinformatics in Karunya University in India was started in the year 2005. The objective is to provide excellent teaching, learning including practical training, research facilities and consultancy services in the frontier areas of Bioinformatics.
The course is designed to provide advanced research and industrial exposure to the students and it covers frontier areas like biopharmaceutics, computational biology, enzyme engineering, database management systems, development of algorithms, machine learning approaches, data mining and warehousing, genomics & proteomics, molecular modeling & drug design, molecular phylogeny, neural networks, computer simulations, systems biology, artificial intelligence and nanobiotechnology.
PROGRAMS OFFERED:
The Department of Bioinformatics offers the following 4 years undergraduate B.Tech. Programmes and 2 years postgraduate M.Tech. Programmes:
- B.Tech. Bioinformatics
- M.Tech. Bioinformatics
- M.Phil Bioinformatics
- Ph.D. Bioinformatics
For eligibility and other details please refer http://www.karunya.edu
The department is conducting 2 days National Conference on Computational Biology on 22nd & 23rd August 2008. For details contact jannet_r@karunya.edu or prems.bioinfo@gmail.com
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We would like to invite you to apply for travel fellowships available for participants in the 4th ISCB Student Council Symposium at ISMB 2008 in Toronto (Canada). We are able to provide 7 travel fellowships worth $1,000 USD each.
The deadline for applications is May 26th. This is also the abstract submission closing date.
Keynotes by Mark Gerstein, Timothy Hughes and Burkhard Rost as well as a panel discussion on "Career Paths in Bioinformatics and Computational Biology" with panelists Philip Bourne, Alfonso Valencia, Jong Bhak and Richard Wintle are part of the updated agenda.
We are happy to announce that we will again publish a selection of outstanding abstracts as a supplement to BMC Bioinformatics.
FOR MORE INFORMATION:
[link]
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LOCALE: Online @ Bioinformatics.Org
DATES: May 19-23, 2008
Join Harvard University Professor Cheng Li in this online workshop on dChip, his software application for gene expression and SNP genotyping analysis. We will cover topics such as importing arrays, performing normalization, model based expression calculations, gene and SNP filtering, clustering, linkage and LOH analysis, and much more.
FOR MORE INFORMATION:
[link]
NB: This course will not be offered on a regular basis, and seats are limited.
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| Acknowledgments |
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We wish to thank the following for their support:
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