Bioinformatics meets systems biology

A report on the Fifth International Workshop on Bioinformatics and Systems Biology, Berlin, Germany, 22-25 August 2005.     

Bioinformatics and systems biology research update from the 15<Superscript>th</Superscript> International Conference on Bioinformatics (InCoB2016)

The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20–22, 2017.     

The European Bioinformatics Institute web site: a new view

SUMMARY: The European Bioinformatics Institute (EBI), and outstation of the European Molecular Biology laboratory, has revamped its web site for the second time since 1997 in order to address increased user demand as well as establishing better uniformity and easier accessibility for the ever growing number of users and services it offers to the community. A GRID-like hardware infrastructure has been put in place to provide round the clock services in a redundant and reliable fashion. AVAILABILITY: http://www.ebi.ac.uk/     

Workshop--Predicting the structure of biological molecules

This April, in Cambridge (UK), principal investigators from the Mathematical Biology Group of the Medical Research Council's National Institute of Medical Research organized a workshop in structural bioinformatics at the Centre for Mathematical Sciences. Bioinformatics researchers of several nationalities from labs around the country presented and discussed their computational work in biomolecular structure prediction and analysis, and in protein evolution. The meeting was intensive and lively and gave attendees an overview of the healthy state of protein bioinformatics in the UK.     

Report from the First Snake Genomics and Integrative Biology Meeting

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.     

Meeting review: 2002 O'Reilly Bioinformatics Technology Conference

At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference [14]. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.     

Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server

Conferences in computational biology continue to provide tutorials on classical and new methods in the field. This can be taken as an indicator that education is still a bottleneck in our field's process of becoming an established scientific discipline. Bielefeld University has been one of the early providers of bioinformatics education, both locally and via the internet. The Bielefeld Bioinformatics Server (BiBiServ) offers a variety of older and new materials. Here, we report on two online courses made available recently, one introductory and one on the advanced level: (i) SADR: Sequence Analysis with Distributed Resources (http://bibiserv.techfak.uni-bielefeld.de/sadr/) and (ii) ADP: Algebraic Dynamic Programming in Bioinformatics (http://bibiserv.techfak.uni-bielefeld.de/dpcourse/).     

Integrative proteomics: structure, function, and interaction report on the 3rd joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, July 2006

This report summarizes the highlights of the recent British Society for Proteome Research (BSPR) meeting jointly organized with the European Bioinformatics Institute (EBI) which was held at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK in July 2006. This was the third annual scientific meeting organized by the BSPR and EBI and the theme of this years meeting was Integrative Proteomics: Structure, function and interaction. A wealth of local and overseas speakers were invited to discuss both their own work and specific challenges present in modern day proteomic based experiments.     

Grand network convergence

A report of the Systems Biology: Networks meeting, Cold Spring Harbor, USA, 22-26 March 2011.     

生物信息学在发现新基因方面的应用

自生物信息学作为一门交叉学科诞生以来,其在计算机、农业和生命科学等各方面发挥了重要的作用,在后基因组时代,更是成为发现新基因的重要手段。对生物信息学的概况做了回顾与展望,并简述了生物信息学近年在发现新基因方面所取得的成果。     

Enhancing Bioinformatics and Genomics Courses: Building Capacity and Skills via Lab Meeting Activities

Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1-day lab meeting in the framework of two previously organized 3-month courses on “Bioinformatics and Genome Analyses”. The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self-confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses.     

5th BSPR‐EBI Meeting,Proteomics: From Technology to New Biology 8–10 July 2008, Wellcome Trust Conference Centre,Hinxton, Cambridge,UK

This paper reports on the 5^th joint British Society for Proteome Research (BSPR) and European Bioinformatics Institute (EBI) meeting which took place at the Wellcome Trust Conference Centre, Cambridge, UK, from the 8^th to 10^th July, 2008. As in previous years, the meeting attracted leading experts in the field who presented the latest cutting edge in proteomics. The meeting was entitled “Proteomics: From Technology to New Biology” taking into account the major transition proteomics has undergone in the past few years. In particular, the use of multiple reaction monitoring (MRM)‐based targeted experiments for absolute quantification and validation of proteins was the hot topic of the meeting. Attended by some 250 delegates, the conference was extremely well organised and provided a great opportunity for discussion and initiation of new collaborations.     

生物信息数据库知识产权保护初探

生物信息技术是当今生命科学乃至整个自然科学的重大前沿领域之一,生物信息数据库是生物信息技术中非常重要的部分,对生命科学的发展起着重要的推动作用。本文叙述了生物信息数据库的特点及国内外知识产权保护现状,初步讨论了生物信息数据库知识产权保护中存在的问题,提出了保护我国生物信息数据库的建议。     

Bioinformatics

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.     

A Quick Guide for Building a Successful Bioinformatics Community

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).     

Bioinformatics 2000

A report from the Bioinformatics 2000 conference [], held in Elsinore, Denmark, 27-30 April, 2000.