Industry Partner Talks

Open science needs open scientists: an ever-increasing inter- dependence

Dr. Robert Davey

Group Leader, Data Infrastructure & Algorithms , The Genome Analysis Centre (TGAC), United Kingdom

In recent years, scientific research has experienced an interesting juxtaposition. There is increasing pressure from funding bodies to make research data accessible. Researchers also need the increasingly sensational track records published in high-impact journals to ensure continued project support and/or tenure.

Pressure to release data by funders, whilst obviously a step in the right direction, represents a formidably large stick but a depressingly small carrot which results in simply another tedious hurdle to getting research published rather than a vehicle to get recognition. The constant push for papers in journals with perceived impact and prestige, whilst still seen as a key assessment mechanism for a researcher’s career, promotes a closed door approach and a touch of paranoia, with research becoming a competitive endeavour rather than a mutually beneficial collaborative one.

Thankfully, a new breed of researchers at all career stages, from graduate to PI, who can see these mutual benefits of sharing their work openly are becoming greater in number and more vocal by the day. Open source code, open data, powerful tools and infrastructure, social networks, and open access publishing all play a part in the ecosystems of the Open Science movement.

Biography

Robert joined TGAC in February 2010 as the lead software engineer on the MISO lab information management (LIMS) project, which was released to the community as an open source framework for tracking sequencing experiments in 2012. He went on to become the Core Bioinformatics Project Leader, managing a team of developers to advance MISO as well as new projects into data infrastructure and management, and the genomic data visualisation tool, TGAC Browser. Robert was appointed as Data Infrastructure and Algorithms Group Leader in late 2012. Robert's main interests are in enterprise-grade software development, data management and associated HPC infrastructure, sequence analysis and quality control pipelines, novel visualisation strategies for sequencing and biological data, metadata and the Semantic Web, and the open source ethos. Prior to joining TGAC, he was a post-doctoral researcher at the Institute of Food Research (IFR) in the National Collection of Yeast Cultures (NCYC) group, providing analytical tools and bioinformatics support to help drive this important national capability. He completed his degree in Microbiology and his PhD in Bioinformatics at the University of East Anglia (UEA), the latter developing algorithms for assessing the gene content of bacterial organisms using Comparative Genomic Hybridisation microarrays. The Data Infrastructure and Algorithms group focuses on research into understanding how best to manage, represent and analyse data for open science, as well as exploring new hardware, algorithms and methodologies to develop tools to push the boundaries of data-driven informatics in the life sciences. The team applies their research expertise to develop infrastructure platforms for data and software dissemination and publication, assembly algorithms for viral and microbial metagenomics, large-scale data visualisation, and best practice and training in bioinformatics.


Publishing in the digital age – introducing the ISCB Community Journal

Mr. Michael Markie

Associate publisher, F1000Research Ltd.

Despite moving from paper to pixels, the publication of scientific research has not harnessed the full potential of the internet and remains remarkably similar to the first journal published 350 years ago. Journals at large still use a system that’s rooted in the pre-web era of print and they are often criticised for stifling academic progress. The web provides the opportunity to communicate science much more efficiently and allows us to address some of the most talked about issues around journals such as anonymous peer review, delays in publication, and reproducibility. F1000Research is an online only open science platform that sets out to tackle these issues through immediate and transparent publishing, and is now collaborating with the ISCB to publish the ISCB Community Journal, which will support the open publication of research in a range of formats from select ISCB conferences and COSIs.

Biography

Michael Markie is an open science and open data advocate and is currently the associate publisher for F1000Research, an author led open science platform that offers immediate publication, transparent peer review (post-publication) and full data deposition and sharing. Michael’s role at F1000 is to help build and innovate new digital solutions for sharing scientific research, and in particular spends a lot of time doing academic outreach and collaborating with the scientific community to identify new ways to improve how scientific research is disseminated and made publically available.