EMBnet.news
type: channel
publisher: EMBnet
language: en-US
publication name: EMBnet.news
issn: 1023-4144
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items: EMBnet.news 15.4
items: Editorial
items: Utopia Documents and The Semantic Biochemical Journal experiment
items: wEMBOSS and wrappers4EMBOSS
items: BITS 2010 - Bioinformatics and Computational Biology for Life Sciences research
items: Bioinformatics at Nile University: Perspectives for Egypt and the Whole Region
items: The New South Wales Systems Biology Initiative
items: Centre for Proteomic & Genomic Research: World Class Biotech Made in Africa
items: The EMBnet Annual General Meeting 2009 and EMBnet-RIBIO joint conference
items: Argentinian EMBnet node: progress report
items: Brazilian EMBnet Node: progress report
items: Chilean EMBnet node: progress report
items: Colombian EMBnet node: progress report
items: Greek EMBnet node: progress report
items: Pakistan EMBnet node: progress report
items: Spanish EMBnet node: progress report
items: Sri Lankan EMBnet node: progress report
items: ILRI-BecA , EMBnet specialist node: progress report
items: UMBER - University of Manchester Bioinformatics Education & Research
items: Jornadas de Bioinfomática JB2009 - November 3rd-6th 2009
items: Next Generation Sequencing Workshop.
items: High Throughput Sequencing and the IT architecture (Part 1 : Volume dimensioning and filesystems)
items: Protein Spotlight 113

EMBnet.news 15.4
type: item
creator: EMBnet news
rights: Copyright (c)
date: 2010-03-11
publication date: 2010-03-11
volume: 15
number: 4

Editorial
type: item
creator: Erik Bongcam-Rudloff
rights: Copyright (c)
date: 2010-03-16
publication date: 2010-03-16
volume: 15
number: 4
starting page: 2

Utopia Documents and The Semantic Biochemical Journal experiment
type: item
description: 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.
creator: Teresa K Attwood
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 3
ending page: 6

wEMBOSS and wrappers4EMBOSS
type: item
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creator: Guy Bottu
creator: Marc Colet
rights: Copyright (c)
date: 2010-02-15
publication date: 2010-02-15
volume: 15
number: 4
starting page: 7

BITS 2010 - Bioinformatics and Computational Biology for Life Sciences research
type: item
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creator: Domenica D'Elia
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 8
ending page: 9

Bioinformatics at Nile University: Perspectives for Egypt and the Whole Region
type: item
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creator: Mohamed Abouelhoda
creator: Moustafa Ghanem
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 10
ending page: 11

The New South Wales Systems Biology Initiative
type: item
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creator: Bruno Andre Gaeta
creator: Marc Wilkins
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 11
ending page: 12

Centre for Proteomic & Genomic Research: World Class Biotech Made in Africa
type: item
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creator: Reinhard Hiller
creator: Judit Kumuthini
rights: Copyright (c)
date: 2010-02-12
publication date: 2010-02-12
volume: 15
number: 4
starting page: 13

The EMBnet Annual General Meeting 2009 and EMBnet-RIBIO joint conference
type: item
description: 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.
creator: Jose R. Valverde
rights: Copyright (c)
date: 2010-02-08
publication date: 2010-02-08
volume: 15
number: 4
starting page: 14
ending page: 23

Argentinian EMBnet node: progress report
type: item
description: 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.
creator: Oscar Grau
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 24

Brazilian EMBnet Node: progress report
type: item
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creator: Ana Tereza Vasconcelos
creator: Goran Neshich
creator: Wim M. Degrave
rights: Copyright (c)
date: 2010-02-10
publication date: 2010-02-10
volume: 15
number: 4
starting page: 25
ending page: 31

Chilean EMBnet node: progress report
type: item
description: 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.
creator: Cristian J. Salgado
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 31
ending page: 32

Colombian EMBnet node: progress report
type: item
description: 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.
creator: Emiliano Barreto
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 33

Greek EMBnet node: progress report
type: item
description: 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.
creator: Sophia Kossida
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 34

Pakistan EMBnet node: progress report
type: item
description: 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.
creator: Nazim Rahman
creator: Shahid N. Chohan
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 35
ending page: 36

Spanish EMBnet node: progress report
type: item
description: 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....
creator: Jose R Valverde
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 36
ending page: 37

Sri Lankan EMBnet node: progress report
type: item
description: 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.
creator: Kanchana S. Senanayake
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 38

ILRI-BecA , EMBnet specialist node: progress report
type: item
description: 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.
creator: Etienne de Villiers
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 39
ending page: 40

UMBER - University of Manchester Bioinformatics Education & Research
type: item
description: 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.
creator: Teresa K Attwood
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 41
ending page: 42

Jornadas de Bioinfomática JB2009 - November 3rd-6th 2009
type: item
description: 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....
creator: Pedro L. Fernandes
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 43

Next Generation Sequencing Workshop.
type: item
description: 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.
creator: Jose R. Valverde
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 44
ending page: 50

High Throughput Sequencing and the IT architecture (Part 1 : Volume dimensioning and filesystems)
type: item
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creator: George Magklaras
rights: Copyright (c)
date: 2010-02-03
publication date: 2010-02-03
volume: 15
number: 4
starting page: 51
ending page: 55

Protein Spotlight 113
type: item
creator: EMBnet news
rights: Copyright (c)
date: 2010-02-08
publication date: 2010-02-08
volume: 15
number: 4
starting page: 56
ending page: 57