Conquering computational challenges of omics data and post-ENCODE paradigms

A report on the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), held in Berlin, Germany, July 21-23, 2013.     

Computational biology: plus c'est la même chose,plus ça change

A report on the joint 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)/10th Annual European Conference on Computational Biology (ECCB) meetings and the 7th International Society for Computational Biology Student Council Symposium, Vienna, Austria, 15-19 July 2011.     

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.Open in a separate window     

Bioinformatics: living on the edge

A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012.     

From sequence to structure to networks

A report on the 7th European Conference on Computational Biology (ECCB), Cagliari, Italy, 22-26 September 2008.     

Putting the 'bio' into bioinformatics

A report on the 13th Annual Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, USA, 25-29 June 2005.     

The intelligence in developing systems for molecular biology

A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.     

Understanding biology through intelligent systems

A report on the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Edmonton, Canada, 3-7 August 2002.     

An illuminated view of molecular biology

A report on the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 7th Special Interest Group meeting on Alternative Splicing, Boston, USA, 9-13 July 2010.     

The rise of translational bioinformatics

ABSTRACT: A report on the 20th International Conference on Intelligent Systems for Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.     

First Barcelona Conference on Epigenetics and Cancer

The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled “Challenges, opportunities and perspectives” took place November 21–22, 2013 in Barcelona. The 2013 BCEC is the first edition of a series of annual conferences jointly organized by five leading research centers in Barcelona. These centers are the Institute of Predictive and Personalized Medicine of Cancer (IMPPC), the Biomedical Campus Bellvitge with its Program of Epigenetics and Cancer Biology (PEBC), the Centre for Genomic Regulation (CRG), the Institute for Biomedical Research (IRB), and the Molecular Biology Institute of Barcelona (IBMB). Manuel Perucho and Marcus Buschbeck from the Institute of Predictive and Personalized Medicine of Cancer put together the scientific program of the first conference broadly covering all aspects of epigenetic research ranging from fundamental molecular research to drug and biomarker development and clinical application. In one and a half days, 23 talks and 50 posters were presented to a completely booked out audience counting 270 participants.     

GOBLET: The Global Organisation for Bioinformatics Learning,Education and Training

In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.     

GIDMP: Good protein-protein interaction data metamining practice

Studying the interactome is one of the exciting frontiers of proteomics, as shown lately at the recent bioinformatics conferences (for example ISMB 2010, or ECCB 2010). Distribution of data is facilitated by a large number of databases. Metamining databases have been created in order to allow researchers access to several databases in one search, but there are serious difficulties for end users to evaluate the metamining effort. Therefore we suggest a new standard, “Good Interaction Data Metamining Practice” (GIDMP), which could be easily automated and requires only very minor inclusion of statistical data on each database homepage. Widespread adoption of the GIDMP standard would provide users with:

Do you do text?

Retrieving information from text has become an important areain bioinformatics, and not too surprisingly, this journal haspublished more than 30 papers on this topic since the firstarticle published by the journal in 1998. In addition, ISCB(International Society for Computational Biology) (www.iscb.org)has organized special sessions in the ISMB conferences (IntelligentSystems for Molecular Biology, see www.iscb.org/ismb2005) anda specialized interest group (www.pdg.cnb.uam.es/BioLink/) forthe last five years. In parallel, major computer science conferencesin related areas have begun     

Discovering the intelligence in molecular biology

The Third International Conference on Intelligent Systems in Molecular Biology was truly an outstanding event. Computational methods in molecular biology have reached a new level of maturity and utility, resulting in many high-impact applications. The success of this meeting bodes well for the rapid and continuing development of computational methods, intelligent systems and information-based approaches for the biosciences. The basic technology, originally most often applied to ‘feasibility’ problems, is now dealing effectively with the most difficult real-wold problems. Significant progress has been made in understanding protein-structure information, structural classification, and how functional information and the relevant features of active-site geometry can be gleaned from structures by automated computational approaches. The value and limits of homology-based methods, and the ability to classify proteins by structure in the absence of homology, have reached a new level of sophistication. New methods for covariation analysis in the folding of large structures such as RNAs have shown remarkably good results, indicating the long-term potential to understand very complicated molecules and multimolecular complexes using computational means. Novel methods, such as HMMs, context-free grammars and the uses of mutual information theory, have taken center stage as highly valuable tools in our quest to represent and characterize biological information. A focus on creative uses of intelligent systems technologies and the trend toward biological application will undoubtedly continue and grow at the 1996 ISMB meeting in St Louis.     

Research of a holiday kind: A clinical trial gone awry: the Chocolate Happiness Undergoing More Pleasantness (CHUMP) study

The randomized controlled trial is the “gold standard” for evaluating the benefits and harms of interventions. The Chocolate Happiness Undergoing More Pleasantness (CHUMP) study was designed to compare the effects of dark chocolate, milk chocolate and normal chocolate consumption on happiness. Although the intention-to-treat analysis showed that participants who received either dark or milk chocolate were happier than those who received no additional chocolate, the actual-consumption analysis showed that there were no differences between any of the groups. The reason for this result is that many participants switched groups mid-study because of their personal chocolate preferences. Although the CHUMP study was pleasurable, it demonstrated the difficulties associated with performing a truly blinded clinical trial.The randomized controlled trial is the “gold standard” for testing the beneficial and harmful effects of interventions. There has been a growing concern in the literature about the potential for bias during randomization of participants in clinical trials.^1–5 I designed the Chocolate Happiness Undergoing More Pleasantness (CHUMP) study to compare the effects of dark chocolate, milk chocolate and “normal” chocolate consumption on happiness. The CHUMP study was a double-blinded clinical trial, and it demonstrated the difficulties associated with performing a truly blinded clinical trial.     

“Broadband” Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development

A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment and sustainable development in Africa. The “omics” fields, especially genomics, are increasingly dependent on the effective interpretation of large and complex sets of data. Despite abundant natural resources and population sizes comparable with many first-world countries from which talent could be drawn, countries in Africa still lag far behind the rest of the world in terms of specialized skills development. Moreover, there are serious concerns about disparities between countries within the continent. The multidisciplinary nature of the bioinformatics field, coupled with rare and depleting expertise, is a critical problem for the advancement of bioinformatics in Africa. We propose a formalized matchmaking system, which is aimed at reversing this trend, by introducing the Knowledge Transfer Programme (KTP). Instead of individual researchers travelling to other labs to learn, researchers with desirable skills are invited to join African research groups for six weeks to six months. Visiting researchers or trainers will pass on their expertise to multiple people simultaneously in their local environments, thus increasing the efficiency of knowledge transference. In return, visiting researchers have the opportunity to develop professional contacts, gain industry work experience, work with novel datasets, and strengthen and support their ongoing research. The KTP develops a network with a centralized hub through which groups and individuals are put into contact with one another and exchanges are facilitated by connecting both parties with potential funding sources.This is part of the PLOS Computational Biology Education collection.     

Temporal Stability and the Effects of Training on Saccade Latency in “Express Saccade Makers”

The temporal stability of saccade latency, and the effects of training, particularly in “express saccade makers” (ESMs), has received little attention. ESMs are healthy, naïve, adults, who persist in executing very many low latency “express saccades” (ES; saccades with latency of 80 ms to 130 ms), in conditions designed to suppress such responses. We investigated the stability of ES production (%ES) in 59 ESM and 54 non-ESM participants in overlap tasks. Within a single session, the intraclass correlation coefficient (ICC) for %ES in two runs of 200 trials was 0.97 (p<0.001); participants in whom >30% of saccades over the two runs were ES, were classified as ESMs. For 60 participants tested over two sessions 12 weeks apart, and 30 participants tested in three sessions over approximately six months, the ICC for %ES was uniformly high (0.95, p<0.001 and 0.97, p<0.001 respectively) and participants behaved consistently with their initial classification. Fourteen participants (7 ESMs) were then exposed to training consisting of either gap or overlap tasks. Training increased %ES in both groups. However, when tested in overlap tasks, it was not sufficient to transform Normal participants into ESMs. We conclude that the pattern of saccade behaviour exhibited by ESMs constitutes a stable and distinct oculomotor phenotype.     

Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions

The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.