Archive by category | Data availability

Nature Physics calls for support of the arXiv preprint server

Nature Physics calls for support of the arXiv preprint server

Funding of the arXiv preprint server must now be shared by more of its users, says Nature Physics in its March Editorial (6, 147; 2010) From the Editorial: The arXiv preprint server has become central to the working lives of most physicists: ‘checking the arXiv’ is the starting point of many a daily routine. Founded by Paul Ginsparg, the arXiv has expanded to include not only physics — astrophysics, condensed matter, and high-energy physics being heavily represented — but also mathematics, computer science, quantitative biology and even quantitative finance. The arXiv now hosts nearly 600,000 preprints from 101,000 registered submitters  … Read more

Nature Medicine on access to and integrity of data

Nature Medicine on access to and integrity of data

Everybody agrees that ensuring the integrity and accessibility of research data is crucial for scientific progress. Agreeing on the best way to do so is the hard part, says Nature Medicine in its February Editorial ( 16, 131; 2010). Technological advances have enabled researchers to tackle questions that involve generating vast amounts of data, posing challenges concerning data analysis, manipulation, annotation, sharing and storage that researchers, institutions, funders and journals have not yet fully grasped. How should data be annotated before being stored in a database so that it can be as useful as possible to other researchers? Should data-sharing  … Read more

Are smartphones making inroads into the laboratory?

Are smartphones making inroads into the laboratory?

Mobile computing platforms such as the iPhone are beginning to make inroads into the laboratory—serious prospect or fairy tale? So asks Nature Methods (7, 87; 2010), starting its February Editorial in traditional genre style: “Once upon a time phones were used exclusively for conversing with other people, and computers ran software applications. The computer became an indispensable tool in the laboratory while the phone developed into a mobile device that has disrupted countless lectures at scientific conferences. But recently researchers can be seen talking on their computer and using their cell phone for running fancy—and sometimes powerful—software programs. This metamorphosis  … Read more

Nature Genetics on conclusion by exclusion

Nature Genetics on conclusion by exclusion

“Science is a way to distinguish things we know not to be true from other things. Large challenges lie ahead as we apply the scientific method to understanding biochemical systems, cellular organization and the functions of complex organs such as the brain.” So begins the February Editorial in Nature Genetics (42, 95; 2010). If the success of the early years of molecular biology can be attributed to the simplicity of the problems to solve, combined with rigorous experimental design including disprovable hypotheses and decisive experiments, what of todays immensely more complex scientific landscape and greatly increased number of scientists, not  … Read more

Protein Data Bank policies for disputed structures

Helen M. Berman, director of the RCSB (Research Collabatory for Structural Bioinformatics) Protein Data Bank, and co-authors wrote a Correspondence to Nature ( 463, 425; 2010) to clarify the PDB’s correction procedures and policies in the light of a current investigation. Their letter is reproduced here.  Read more

Integrating with integrity, according to Nature Genetics

Integrating with integrity, according to Nature Genetics

Data worthy of integration with the results of other researchers need to be prepared to explicit export standards, linked to appropriate metadata and offered with field-specific caveats for use. The Editorial in the January edition of Nature Genetics ( 42, 1; 2010) explores the extent to which, to be useful at generating new analyses and hypotheses, data sharing needs to be about standardized formats as much as simply being made ‘available’. For example, the Editorial states, “Sample sizes, selection criteria, statistical significance, number of hypotheses tested, normalization and scaling procedures, read depth and sequence quality scores are all important considerations  … Read more

Nature Biotechnology focus on synthetic biology

Nature Biotechnology focus on synthetic biology

The December 2009 issue of Nature Biotechnology focuses on synthetic biology, in a special feature (subscription) containing news, opinion, comment and research articles on the topic. The focus discusses some of the progress in synthetic biology towards practical applications, as this latest iteration of genetic engineering, although still in its infancy, offers the prospect of the design and construction of new life forms from biological parts, devices and systems. If, however, you aren’t sure exactly what synthetic biology is, Nature Biotechnology asked 20 specialists for their definitions, so you can take your pick. The Editorial that begins the focus asserts  … Read more

Nature Cell Biology joins call for microattribution of datasets

Nature Cell Biology (11,1273; 2009) joins in the call for ‘microattribution’ in its November Editorial, stating that reference datasets should be accessible independently of scientific papers in a citable form. The problem, from a cell biological perspective:  … Read more

Data producers deserve citation credit, says Nature Genetics

Datasets released to public databases in advance of (or with) research publications should be given digital object identifiers to allow databases and journals to give quantitative citation credit to the data producers and curators, according to the October Editorial of Nature Genetics (41, 1045; 2009) .  Read more

Nature Biotechnology: Personal genome data on the line

Continuing the theme of yesterday’s post about data sharing, Nature Biotechnology is running an Editorial this month (Nature Biotech. 27, 777; 2009), ‘DNA confidential’, pointing out that as “the cost of human genome sequencing plunges and large-scale genome-phenotype studies become possible, society should do more to reward those individuals who choose to disclose their data, despite the risks”. The Editorial continues:  … Read more