Posts tagged: Conferences

All systems go at ICSB 2014 and the Great GigaScience and Galaxy (G3) workshop

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The 2014 International Conference on Systems Biology (ICSB) was hosted in Australia’s most livable city and event, sport, culture and food capital – that is Melbourne, with GigaScience being proud to be one of the media partners. Stem cell biology was a major theme on the first day, and kicked off to a strong start with Huck Hui Ng (Executive Director  of the Genome Institute of Singapore) giving a great overview of stem cell systems biology. Ng explained how his lab has set up high-throughput capabilities to further understand stem cell pluripotency. Ng’s lab has been able to show that maintenance of human embryonic stem cell stability is governed by – proteins, TFs and co-factors, mediators of …

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Ain’t No Party like a Bring Your Own Data Party!

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Data Club is Gonna Show You How
As science is supposed to be about “standing on the shoulders of giants”, we all know sharing scientific data should be a good thing, but there are obviously large technical and cultural challenges holding things back. Things are a long way from the Jimmy Wales “Imagine a world in which every single person on the planet is given free access to the sum of all human knowledge” utopian dream, but some research fields (e.g. genomics) have done a better job making data available than others. Unfortunately sharing complicated scientific data usually isn’t as easy as just dumping it in a dropbox folder, and to be reused …

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Continuing the push beyond static documents. ISMB, and more on our “What Bioinformaticians need to know about digital publishing beyond the PDF2” workshop

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Boston 2014: More than a (Bioinformatics) Feeling
Following from our previous posting on BOSC, our birthday and the BMC Open Data award party in Boston, on top of having to dash between the many great talks and sessions at ISMB, we were kept even busier than usual helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop at the end of the conference. Coming in the year that Illumina are hoping to make human clinical genome sequencing affordable with new sequencing platforms, one noticeable trend this year was a larger …

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Bioinformatics, Birthdays, and Booze at Boston BOSC.

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Birthdays are always emotional. The GigaScience team are on their way back from the always jam packed ISMB meeting and its satellite SIGs. This year was a particularly event filled one, with our second birthday, the BMC open data award and drinks reception, and our “What Bioinformaticians need to know about digital publishing beyond the PDF2″ workshop all falling during the meeting. The SIGs were brilliant as always, and we had additional involvement this year, promoting and building on our AFP (Advanced Functional Prediction) series tied in with the SIG of the same name, and sponsoring BOSC (the Bioinformatics Open Source Conference) …

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From function “unknown” to “known”: First papers in our Automated Function Prediction series

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Editors: Mark Wass (University of Kent, UK), Iddo Friedberg (Miami University, Oxford, Ohio, USA), Predrag Radivojac (Indiana University, Bloomington, Indiana, USA)

A key to understanding life at the molecular level is based on accurate protein annotation at the functional level. However, due to the explosion of genomic sequencing data an inherent difficulty and expense exists to scale-up and biologically characterise the plethora of genes and proteins of unknown function – one problem of which is computational annotation of protein function. Genomic sequencing data coupled with high-throughput experimental data has created new challenges and opportunities for function prediction. The Automated Function Prediction Special Interest Group (AFP-SIG) brings together computational and experimental biologists, as well as biocurators, who are dealing with the …

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Rewarding Reproducibility: First Papers in our Galaxy Series utilizing our GigaGalaxy platform

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Push the button! GigaScience moves toward more interactive articles

Research articles are being published with increasingly large and complicated supporting datasets, together with the software code used in analyses of the data. However, there is a growing number of studies reporting the inability to reproduce previously published findings which may, at least in part, be responsible for the increasing rate of retractions that Bjorn Brembs has calculated will overtake the number of papers published some time in the mid-2040s. Furthermore, there is an awareness of the “reproducibility gap” within the scientific community, with Francis Collins of the NIH

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A GigaGathering at ICG8 in the era of big data and crowdsourcing

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As the GigaScience journal moves from strength-to-strength, with that comes the expansion of the editorial and data management teams that are now spanning three continents – and what better way to meet than at the 8th International Conference on Genomics (ICG8) in Shenzhen, China, co-organised by the BGI and GigaScience. Held at the Thunderbirdsesque Vanke International Conference Centre in the popular seaside resort of Dameisha, this year’s meeting covered a range of topics including new innovations and technologies, big data management, crowdsourcing, animal and crop genomics, as well as informatics and metagenomics, to name a few.

George Church was the highlight on the first day, who not surprisingly, gave a fascinating keynote on his amazing technology developments …

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More on our ISMB workshop: What Bioinformaticians need to know about digital publishing beyond the PDF

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Big Data Publishing (credit Jenny Cham, CC-BY)
As mentioned in our previous posting, on top of the many great talks and sessions we attended at ISMB in Berlin last month, we were kept even busy helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop. Most of the heavy lifting has to be credited to the hard work of Marco Roos, but the other organisers included Oscar Corcho, Carole Goble, Barend Mons, Jun Zhao and Erik Schultes, and we had a ridiculously overqualified …

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Bioinformaticians breaking down barriers in Berlin

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Open Science flourishes at BOSC and ISMB
It’s been a busy couple of weeks for GigaScience, with our 1st birthday, publication of a special anniversary print issue sponsored by Aspera, and publication of the (unusually reviewed) Assemblathon2 paper. These all spanned and were coordinated with the ISMB meeting in Berlin, the yearly gathering of the computational biology community. GigaScience was present through the pre-conference SIGs (particularly BOSC and AFP), as well the main conference, co-organizing and speaking at a special …

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GigaBirthday at ISMB

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GigaScience reaches its first anniversary of publication, and achieves several milestones in changing how life science research is published

One year on from our launch, we are unveiling new features and functionality at the Intelligent Systems for Molecular Biology (ISMB) meeting at the ICC in Berlin (pictured) this week. As well as a print issue celebrating the best of the last year, we are announcing new features and tools, along with a new data analysis platform, GigaGalaxy. GigaGalaxy is an online platform that supports the reproducibility of data analyses. It provides a means to share computational tools and workflows that further document and reproduce data analyses reported in papers …

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