Nature Methods has published popular analysis tools to make sense of the ever-increasing amount of high throughput (HTP) sequencing data. Some tools in this field have a short half life, due to pressure to always improve and innovate, others have staying power. Let’s look back over some of the highlights in our pages. Read more
Software plays an important role in scientific research, and published studies increasingly rely on custom software code developed by authors. This calls for better transparency in research articles and improved access to the software and code itself. Read more
A large proportion of original research published in Nature Methods relies to varying degress on custom algorithms and software developed by the authors. Here we provide guidance on our relevant material sharing and reporting policies. Read more
It is no secret that imaging, and microscopy in particular, represents a substantial fraction of the manuscripts published in Nature Methods. Our very first focus issue, in fact, was on fluorescence imaging. When that focus was published in 2005 the term ‘bioimage informatics’ didn’t even exist. Even today, the term isn’t widely used and, unlike many other bioinformaticians, those who work on the development of algorithms and software tools for analysis of biological image data have few dedicated venues for discussing or publishing their work. Read more
When using or developing experimental and observational methods it is crucial to assess the method performance in an effort to ensure that the information it provides reflects reality. For experimental biologists this often means conducting carefully chosen control experiments with alternative methods or different experimental settings. More rigorous assessment, particularly for high-throughput or large-scale methods, often requires the use of ‘ground truth’ or ‘gold standard’ data sets. But talk to different people and you will get different answers regarding what ‘ground truth’ or ‘gold standard’ data is. This often includes a nice historical explanation of where the term ‘ground truth’ comes from. Read more
Do you use your iPhone (or other smartphone or mobile computing device) in the lab? This month’s editorial notes how large numbers of scientists seem to have an iPhone or other mobile device capable of running quite sophisticated applications, or apps. Increasing numbers of these apps are targeted at biologists and some are even intended for use at the lab bench; and lists of recommended apps are popping up on blogs and other sites. Check out the links below for a sample. Read more
Don’t be mistaken, Nature Methods’ material sharing policy includes the requirement to make custom-developed software available upon publication. But there are several ways of making software available. We examine the various degrees of disclosure and the choice of formats and try to clarify our position. Let us know if we are heading in the right direction! Read more
