Aspects Of Computational Biology Research Articles

H3ABioNet computational metagenomics workshop in Mauritius: training to analyse microbial diversity for Africa

In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computational metagenomics was organized during the end of 2014 at the University of Mauritius. The workshop offered background on various aspects of computational biology, including databases and algorithms, sequence analysis fundamentals, metagenomics concepts and tools, practical exercises, journal club activities and research seminars. We have discovered a strong interest in metagenomics research across Africa, to advance practical applications both for human health and the environment. We have also realized the great potential to develop genomics and bioinformatics through collaborative efforts across the continent, and the need for further reinforcing the untapped human potential and exploring the natural resources for stronger engagement of local scientific communities, with a view to contributing towards the improvement of human health and well-being for the citizens of Africa.

NGS research and service at the CBU

http://www.bioinfo.no/http://www.uni.no/computing/units/cbuCBU consists of seven research groups and one service group, specialising in different aspects of computational biology. A common denominator in many of our projects are high throughput data sets, with Next Generation Sequencing as a prominent data providing technology. CBU also coordinates the Norwegian Bioinformatics platform that offers both helpdesk support and training to scientists in the field of functional genomics.A natural research focus in Bergen is marine genomics. The recently published genome of cod [1] were accomplished with CBU as an active partner in the bioinformatics work, in particular the assembly of the 454 reads. Through this and other projects special competence on analysis of high-throughput sequencing (in particular, 454) data has been built, as documented in the work to realise the FlowSim tool [2].Metagenomics on samples from extreme environments along the mid-Atlantic ridge is another field of high interest in Bergen, due to the Centre of Geo-biology (a National Centre of Excellence) situated next to CBU. Through this collaboration, new approaches to handle amplicon sequencing datasets from 454 have been developed, and implemented in the AmpliconNoise software tool [3].Through our role in the National bioinformatics helpdesk and our close collaboration with the Norwegian Microarray Consortium, we have extensive experience in designing experiments and analysing gene expression data from high throughput datasets. Both analysis of data in research projects and training that we provide through the Bioinformatics platform and NMC have successfully been based on the J-Express analysis software suite [4].In addition to algorithms and tools, a suitable infrastructure for step-by-step analysis of your workflow, as well as sharing of data, results and methods across disciplines in a project group, is vital for proper utilization of your data. This is the aim of the eSysbio project, and components of the system are currently in use to implement the StoreBioinfo portal for providing high capacity storage for Life Science data sets in NorStore storage resource (national e-infrastructure).Based on the total research experience and expertise of CBU and on the analysis and e-infrastructure competence built in the national network operated over the 9 previous years, we have coordinated an application for establishing a Norwegian node of the ELIXIR pan-European infrastructure network for bioinformatics.

The early introduction of dynamic programming into computational biology.

In 1994–1995, DIMACS sponsored a theme year on computational biology. Among the numerous seminars and workshops was one organized by Alberto Apostolico and Raffaele Giancarlo, recapitulated in their 1998 paper, on the history and motivations for sequence comparison. In my participation in this event, I was led to consider some of the early interactions, at the Centre de recherches mathematiques (CRM) and elsewhere, in the field now known as computational biology. A short time earlier, I had read a 1989 paper by Walter Goad on the impact of Stanislaw Ulam in this field. The penultimate sentence in this article was a quote from Ulam himself ‘I started all this’, which puzzled me greatly. As far as I knew, Ulam had no impact in the early development of the field, and while he gave talks on it at least from 1971 (cf. Ulam, 1972), the distance he defined was already published (Levenshtein, 1965) and the problem he proposed had already been solved, for all intents and purposes, in the molecular biology literature (Needleman and Wunsch, 1970) and elsewhere (Vintsyuk, 1968). I had also read a joint interview of Ulam and Mark Kac by Feigenbaum (1982), and this led me to reflect on this misperception on the part of Ulam (and of Goad), and to crystallize the realization that ironically, Kac, his colleague of many years, had played a crucial, if indirect, role in the earliest development of the field, especially that associated with the Centre de recherches mathematiques (CRM). Despite the fact that Kac had no personal research interest in the field, his encouragement of a number of junior mathematicians, and his role, intentional or not, in bringing researchers together, recur as important influences in several aspects of computational biology, and explain why I dedicate this article to his memory. In presenting some of these thoughts to the DIMACS workshop, focusing on the early 1970s, my understanding of this period was broadened by comments from a number of participants, particularly Jerrold Griggs and Pavel Pevzner, and clarified by the presentation immediately