The FENS Forum: A Good Time to Be in Spain

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FENS

This year is the “Year of Neuroscience” in Spain. As a part of this educational movement and celebration of the most recent flowering of Spanish neuroscience, Barcelona hosted the FENS Forum of Neuroscience. Drawing what the Chair of the Host Committee, Mara Dierssen, described as the largest number of attendees ever, the 8th FENS meeting fostered cross-disciplinary discussion and showcased some of the field’s best science.

Cori Bargmann gave a fascinating plenary lecture on behavior in C. elegans. Most of the talk focused on the nematode’s reproductive (all of her videos were G-rated, though some of her images were for scientific audiences only) and social foraging …

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Searching for the (Open) Source at Long Beach

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As a project with the aim of revolutionizing data dissemination and use, on top of promoting open-access and open-data, open-source is a key part of the open-science equation, and this week GigaScience has been at the Bioinformatics Open Source Conference (BOSC2012 – program here) in Long Beach. Sponsored by the Open Bioinformatics Foundation (O|B|F), BOSC is a satellite of the ISMB – the annual gathering of the worlds computational biology community, and the many pre-conference SIGs (Special Interest Group Sessions) are a good warm-up for …

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GigaScience launches: overseeing the transition from papers to “executable research objects”

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Research papers have been the predominant form of scholarly communication for the past few centuries, and despite moves towards online publication and open access, the process and structure of publication has not fundamentally changed in that time. With biological and biomedical research becoming increasingly data-driven, and the amount of information, computational tools, and code supporting a publication in areas such as genomics and imaging growing at exponential rates, the lack of access to the resources that the paper is built upon is leading to a growing “reproducibility gap”. Recent scandals relating to falsified data that went long undetected (including …

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Lessons From the “Data Publication Spring”: DataCite Summer 2012

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Readers of this blog will be well versed on our and others work using DataCite Digital Object Identifiers (DOIs) to cite data, and this months DataCite summer meeting in Copenhagen was a good opportunity to take stock of the many recent developments in the area of data publication, with the last six months being particularly busy with the number of new data platforms and data journals announced. On top of the many new data-journals already highlighted in our blog (see this posting), Wiley-Blackwell has just entered the data-publication arena with Read more

The (genomics) view from the 57th floor

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In a busy summer for meetings, this month we attended and presented at Bio-IT World Asia conference in Singapore. In this era of more globalized biology, to celebrate the 10th anniversary of the usually Boston based conference series, with Bio-IT World substituted their usual New England lobster for Chili Crab and heading east. The meetings proximity to the Singapore Biopolis (of which we paid a visit), and its location at the 57 story Marina Bay Sands resort (with its rooftop worlds highest infinity pool), were a winning combination in getting an impressive mix of scientists …

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A conference, neuroimaging, and the wealth of computational neuroscience

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I was fortunate in being able to attend 18th Annual Meeting of the Organization for Human Brain Mapping (OHBM2012). It was a nice turnout, especially considering the long distances many of the attendees traveled to attend the conference in Beijing. Very exciting was the record number of Chinese delegates, a trend the organization would like to see continue in the future.

For me, this year was year of the resting state brain. There was an Educational Course and an Oral session devoted to resting state networks, a strong showing of posters, and a number of good talks on this topic in other sessions and workshops that were not strictly “resting state” series. The energy and ideas floating around the OHBM conference last week suggest …

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Adventures in Data Citation: sorghum as a standard for data release

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A correspondence we have contributed to has just been published in the BMC Research Notes “Data standardization, sharing and publication series” on the data-citation and  data-release practices surrounding the Sorghum genome that is available in our GigaDB database and that was published last year in Genome Biology. We use Sorghum as an example to highlight the issues surrounding data release and use strong words, subtitling the paper “sorghum genome data exemplifies the new gold standard”, justified in this case by the considerable efforts the authors made to go beyond the standards of the field …

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Shanghai (Epigenomics) Surprise

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With genetics and genomics being complicated enough, epigenomics adds even more layers of control and regulation of gene expression, and high-throughput global analyses of epigenetic changes further add to the reams of biological information many people are already referring to as the "data-deluge".  As the field is a key part of our “big-data” scope, the GigaScience team was on the road last week for the Shanghai International Conference of Epigenetics in Development and Disease (SICEDD). As the third time this meeting has been held in Shanghai, this year it also merged with 7th Asian Epigenome Alliance meeting, giving it a very interesting flavor of the field over the Asian region and …

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The State of the Curation Nation

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Of the of the many issues needing addressing in this era of the so-called “data deluge” (apologies genomics bingo), on top of the well documented difficulties in computing power, bandwidth and storage keeping pace with data production, less attention has been paid on the efforts required to present and package this biological information to users. The key people managing and integrating this data are Biocurators, and this week is the International Society of Biocuration‘s annual get together at the Biocuration 2012 meeting in Washington DC. With growing challenges in data volumes and heterogeneity – particularly from sequencing technologies and with the promise …

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Genomic Standards Community Go Shenzhen: GigaScience session overview from #GSC13

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Policies and Standards for Reproducible Research: from theory to practice

This month GigaScience co-hosted a session at the Genomic Standards Consortium meeting in Shenzhen on “Policies and Standards for Reproducible Research: from theory to practice. The session brought together a diverse group of speakers with different roles in the production, dissemination and use of data, to discuss all of the issues surrounding the role of policies and standards enabling reproducible research and data sharing. Co-chaired by our editorial board member Susanna-Assunta Sansone, a diverse panel was assembled representing the different stakeholders involved in the data-production cycle, including …

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