Archive by category | Data availability

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.  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 to mention orders of magnitude more computer power? Are we better equipped to generate, experimentally test, and choose or discard competing hypotheses?  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 that can be misunderstood or missed in combining and reanalyzing data. Whether integrative approaches are useful may depend upon whether integration preserves or destroys essential information….  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.  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