Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
Moving toward fully transparent research publications, we suggest several approaches to share research that is instantiated in software written for computers and other laboratory machines. Review, replication, reuse and recognition are all incentives to provide code.
The assertions in a scientific article that invite testing can be specifically tagged for peer reviewers to evaluate relative to the experimental evidence offered. Isolated observations as well as theories that are not yet publishable can be tagged and immediately released like free-floating bubbles. These can then be considered as useful negative results when popped by experiment or as publishable advances when corroborated by further evidence gathered during attempts at refutation.
Although federated cooperation is politically desirable, uniform data quality and standards are essential and should not be reinvented from scratch. The International Cancer Genome Consortium (ICGC) will do well to start with the data standards of The Cancer Genome Atlas (TCGA) and the Pediatric Cancer Genome Consortium if it is to succeed in genomic analysis across cancer types.
In this issue, the Focus on Pan-Cancer Analysis examines the similarities and differences among the genomic and cellular alterations found in the first dozen tumor types to be profiled by The Cancer Genome Atlas (TCGA) Research Network. This first look across cancers offers new tools in genomics and bioinformatics and the prospect of repurposing targeted therapies to be directed by the molecular pathology of tumors in addition to their clinical classification.
Three disciplines—cancer genomics, functional analysis of cancer cells and nuclear reprogramming—have come together to focus on the basic biology of cell commitment in our Nature Conference with the Ludwig Institute for Cancer Research held 25–27 September in Oxford, UK.
The standards set by the US National Institutes of Health (NIH) for the description, registration and stewardship of large biomedical data sets will be an effective lever, if presented in the form of rules, to guide community and commercial solutions for data analysis and reuse.
Far from defending government spending on genomics as an economic stimulus, we celebrate this landmark contribution to our strategic intelligence on the evolving threats to our health, well-being and life on this planet.
Public health needs to be turned over to the public. Participation in genome-enabled research into the determinants of health is an important form of participation in society and a secure way to ensure the constant improvement of healthcare delivery.
An ever-larger proportion of the liability to common and complex disease can be obtained by progressively larger studies. However, for most diseases, the sample sizes required to gain usable predictions will be out of reach of sequencing technologies for the foreseeable future. Array-based genotyping genome-wide association studies (GWAS) still offer a reliable harvest of biological hypotheses for many diseases, together with the secondary benefit of slowly improving prediction.
Cancer genomes are now rapidly yielding to analysis, showing the heterogeneity of the mutational events and processes contributing to disease. This diversity is enormous and occurs at many levels. Consequently, the first clues from exome sequencing will increasingly need to be complemented by integrated analyses and extended to implicate mutations relevant to treatment outcomes.
In this issue, we offer a draft community standard for a postdoctoral career workshop that can be used as a template and resource for career development at any institution. This document addresses the issue of what can be standardized to improve the lot of postdoctoral researchers, given that this is a professional group with diverse objectives that is motivated mainly by scientific curiosity.
