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Utopia Documents and The Semantic Biochemical Journal experiment
Recent technological advances have led to the accumulation of data on an unprecedented scale. Adding to this information overload is the advent of desk-top sequencing, with machines capable of delivering terabytes of data per hour. The problem is, the rush to increase the amounts of information we collect does not in itself bestow a miraculous increase in knowledge. For information to be usable, it needs to be stored and organised in ways that allow us to access it, to analyse it, to annotate it and to relate it to other information. Unfortunately, to date, we have failed to store and organise much of the rapidly accumulating information (whether in databases or documents) in rigorous, principled ways, so that finding what we want and understanding what’s already known become increasingly exhausting, frustrating and costly experiences. In this Letter, we briefly outline a new development with Portland Press Ltd., the so-called Semantic Biochemical Journal experiment [6]. Behind this ‘experiment’ is a new software tool, Utopia Documents, which builds on the Utopia suite described in previous EMBnet.news articles, and elsewhere [e.g., 7-9]. Here, we provide a sketch of these new developments, in order to provide a taster of what can be achieved through academic-journal-publisher collaboration.
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BITS 2010 - Bioinformatics and Computational Biology for Life Sciences research
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Department of Biochemistry and Molecular Biology of the Bari University are pleased to announce the “Seventh Annual General Meeting of the Italian Bioinformatics Society” to be held in Bari, Italy, April 14-16, 2010.
Bioinformatics at Nile University: Perspectives for Egypt and the Whole Region
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{mso-style-noshow:yes; mso-style-priority:99; color:purple; mso-themecolor:followedhyperlink; text-decoration:underline; text-underline:single;} .MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; mso-ascii-font-family:Calibri; mso-hansi-font-family:Calibri; mso-bidi-font-family:Arial; mso-ansi-language:EN-GB; mso-fareast-language:EN-GB;} @page Section1 {size:612.0pt 792.0pt; margin:70.85pt 2.0cm 2.0cm 2.0cm; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> <!--[if gte mso 10]> <![endif]--> Nile University is a non-profit research university established in 2007 as part of the Egyptian Government’s Strategic Plan aiming at building-up an IT society in Egypt. The Center for Informatics Sciences (CIS) at Nile University, www.cis.nileu.edu.eg, was established in January 2008 as a research center dedicated to the development and application of informatics methods for the management and interpretation of scientific information. The center’s research agenda focuses on the areas of health, agriculture, and environment. Currently, CIS has 40 researchers working in six groups including the Bioinformatics one. The research direction and coordination of the groups is led by Dr. Moustafa Ghanem.
The New South Wales Systems Biology Initiative
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The mission of SBI is to become Australia’s foremost centre for Systems Biology, undertaking basic and applied research in the development and application of bioinformatics for genomics and proteomics, and providing collaborative bioinformatics services in these areas.
Centre for Proteomic & Genomic Research: World Class Biotech Made in Africa
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technical expertise, project support and collaborative research capabilities in the genomics and proteomics arena. The organization has a particular interest in translational research and advancing scientific findings from the bench to the market, including a focus on tackling pressing health needs in Africa as well as on improving crops and livestock.
The EMBnet Annual General Meeting 2009 and EMBnet-RIBIO joint conference
The 2009 Annual General Meeting (AGM) of EMBnet took place in the Mayan Riviera, Mexico, during the last week of October 2009. This meeting was held together with the AGM of the Iberoamerican Bioinformatics Network, both sharing and participating equally the associated Scientific meeting, which this year was centered on High Throughput Technologies and Systems Biology. Besides producing a sound scientific event, the 2009 AGMs of both societies have resulted in a wealth of exciting new initiatives which we all hope shall produce a major impact in Bioinformatics worldwide, such as the foundation of the new Iberoamerican Society of Bioinformatics (SOIBIO) or the agreement among major networks, societies and organizations from all over the world to launch an unprecedented coordination initiative.
Argentinian EMBnet node: progress report
Since last AGM a Live CD was released by the late Martin Sarachu that was intended both for demonstrations of wEMBOSS and for people that have had network connections and do not have access to a bio-server.
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mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} --> The Brazilian EMBnet node conducts research and development in Bioinformatics and Computational Biology, with emphasis on creating and applying computational and mathematical methods and models for solving biological problems. Maintain and develop databases and tools in bioinformatics and computational biology to supply the needs of thematic networks and national and international collaboration projects, as well as train personnel and promote technology and innovation transferring.
In the past three years we have held a large number of activities related to bioinformatics and Systems Biology, which have had a big impact on the local scientific community.
The Bioinformatics Center of the Biotechnology Institute at the National University of Colombia (CBIB) provides Bioinformatics tools, databases, training and support to the Colombian research community.
The Bioinformatics and Medical Informatics Team of the Biomedical Research Foundation of the Academy of Athens (BRFAA) is the Greek EMBnet node. It is headed by Sophia Kossida and it is composed of 26 persons including Senior Researchers, PhD candidates, Technicians, Master’s and undergraduate students.
COMSATS Institute of Information Technology (CIIT), Department of Biosciences in Islamabad is the EMBnet Pakistan National Node. The node started in 2006. Following is a brief report of our activities and future goals.
During the last year the Spanish EMBnet node has been active in the Executive Board of EMBnet (see EB report in this issue). Several EMBnet courses have been organised at CNB in Madrid during the period 2008-2009....
The Institute of Biochemistry, Molecular Biology and Biotechnology is an independent institute of the University of Colombo established in 2004. It is located in the main campus of the University of Colombo. Its main activities are in human resource training and research and development in Molecular Life Sciences and allied fields.
ILRI-BecA , EMBnet specialist node: progress report
The mission of ILRI-BecA node is to provide widely used bioinformatics tools, databases and data storage to the east and central African research community through a central Bioinformatics platform.
UMBER - University of Manchester Bioinformatics Education & Research
As a Specialist Node, UMBER receives neither finance nor a mandate from government to serve a national community. Instead, working in an academic institution, our role is to perform research and teaching, the fruits of which labours we offer freely on the Web. Page restrictions forbid a full account of our work in the last 3 years, but here we give a flavour of some of our activities.
Jornadas de Bioinfomática JB2009 - November 3rd-6th 2009
More than a year ago, the Portuguese and Spanish bioinformatics communities decided that they should organize a common conference with the aim of reinforcing existing links and creating new ones....
In November 2009, CASPUR, EMBRACE, EMBnet, the Italian Society of Bioinformatics and UPPMAX allied to organize a workshop on Next Generation Sequencing technologies and data analysis tools focusing on "Building Next Generation Sequencing platforms and pipeline solutions". The workshop took place in Rome and was addressed to Bioinformaticians interested in discussing issues related to the management of platforms and analysis of next-generation sequencing (NGS) data. In addition to lectures from leading scientists in the field, the workshop also included a hands-on session, a “hackaton” where participants could try by themselves some of the tools to solve an unpublished, real world problem in genome sequence assembly. The workshop web site is located at www.nextgensequencing.org.
High Throughput Sequencing and the IT architecture (Part 1 : Volume dimensioning and filesystems)
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font-size:10.0pt; mso-ansi-font-size:10.0pt; mso-bidi-font-size:10.0pt;} @page Section1 {size:612.0pt 792.0pt; margin:70.85pt 2.0cm 2.0cm 2.0cm; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> <!--[if gte mso 10]> <mce:style><! /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} --> Improvements in DNA sequencing technology have reduced the cost and time of sequencing a new genome. The new generation of High Throughput Sequencing (HTS) devices means has provided large impetus to the life science field and genome sequencing is now a necessary first step of many complex research projects with direct implications to the field of medical sequencing, cancer and pathogen vector genomics, epi and meta genomics. However, despite the falling sequencing cost and time outlines, there are other associated costs and difficulties in the process of maintaining a functional data repository on large scale research projects. The new generation of HTS technologies [1] has introduced the need for increased data storage technologies whose capacity is well beyond the average local data storage facilities [2]. In fact, the computing world has produced a new term for this paradigm, that of data intensive computing [2a]. Data storage costs are falling, however a study of the functional specifications of popular HTS equipment, such as Roche's 454 pyrosequencers [3], Illumina's hardware [4] and ABI SOLiD technology [5] suggests that a single high throughput experiment run creates several Tbytes of information. If one takes into account that genome sequencing is often performed repeatedly in order to study genetic variation [6], the capacity of a suitable data archiving facility needs to scale to several Petabytes of information, which is well beyond the scale of most group, departmental, university computing facilities.