Moore's law refers to the trend observed in computing hardware that the number of transistors on a computer chip doubles about every two years, thus effectively doubling computing power. This has been considered quite a rapid increase.

However, this increase pales in comparison to recent and continuing advances in the throughput of DNA sequencing technology that have resulted in an astonishing increase in the production of DNA sequence by biologists. This is certainly true in the field of metagenomics which involves shotgun sequencing of the genomes (or transcriptomes) of all the organisms in an environmental sample. Biologists are adopting this technology at an rate that was completely unanticipated by most people in the field. This is creating a situation where comprehensive analysis of the resulting sequences, whose analysis is far more complex than for single-genome sequence, is becoming computationally intractable with existing resources and pipelines. The Joint Genome Institute's call for large scale (Terabase) "Grand Challenge” metagenomic projects highlights the scale of datasets that people are now discussing.

The editorial in the September issue of Nature Methods discusses this situation and calls for concerted efforts to ameliorate the metagenome-analysis gridlock that appears imminent. The recently formed M5 (metagenomics, metadata, metaanalysis, multiscale-models and metainfrastructure) Consortium will be proposing a promising solution, the 'M5 Platform', later this year. We hope these efforts will find support and be successful at ensuring this deluge of valuable data is analyzed efficiently and productively.

Posted by Daniel Evanko at 10:27 AM | Permalink | Comments (0) | TrackBacks (0)

The editorial in the August issue of Nature Methods discusses an issue that comes up when computational biologists—or anyone else for that matter—wants to report a novel algorithm that biologists may want to use in their research. Specifically, whether or not to supply a named software implementation of their algorithm that biologists can use.

As part of our standard material sharing policy, Nature Methods generally requires that authors provide a useable software program implementing any new algorithm that is integral to a method they're reporting. But we have never said anything about naming the software.

It recently came to our attention that there are a number of factors that act to discourage authors of new algorithms from naming a software implementation of their algorithm. As discussed in the editorial, this can lead to difficulties later on and in many cases providing a name for the software has benefits that outweigh the potential hazards. Read the editorial and then let us know what you think.

Posted by Daniel Evanko at 01:00 PM | Permalink | Comments (0) | TrackBacks (0)

In July of 2007, we highlighted several popular nonfiction science books on our “summer reading” lists in our Editorial. Given the abundance of nonfiction books on scientific topics, many of which are written for the general public, it was not too hard to identify a short list of stellar examples of science writing. For this month’s Editorial, we sought to highlight fiction books with realistic scientists (even more specifically, biologists) as main characters in laboratory settings.

This did not turn out to be a very easy task, because few books fall under the label of “science in fiction” or “lab lit”, and stories about biologists doing believable biology research are even rarer. The list of books of this sort featured in the Editorial is not comprehensive, but it is perhaps nearly so. If you are interested in finding more books in the science-in-fiction genre, LabLit.com is an excellent resource. This online magazine is edited by Jennifer Rohn, the author of Experimental Heart (one of the books profiled in the Editorial) and a practicing cell biologist at University College London. Rohn was inspired to try to raise the profile of books in this genre after reading Cantor’s Dilemma by Carl Djerassi, when she was in graduate school. LabLit.com has become quite a popular site, and now more than 80 books are profiled on the “lab lit list”. Many of these books have been best-sellers or won awards, indicating that there is interest from the general public in stories about scientists.

Despite the more in-your-face forms of entertainment – television, movies, the internet – an old-fashioned novel is still a source of pleasure for many of us. It’s also a fantastic medium for overturning stereotypes about scientists, and for getting more people interested in science and for educating them about what scientists do. It also allows authors to draw attention to the important issues of ethics and the societal and personal impacts of scientific research. The books highlighted in the July Editorial are great examples of realistic representations of biologists in page-turning stories.

Happy summer reading!

Posted by Allison Doerr at 09:26 AM | Permalink | Comments (0)

The editorial in the April issue of Nature Methods explores the role of methodological developments in the evolution of the scientific method. Some have argued that the ability to collect massive amounts of data and combine this with powerful correlative analyses will make hypothesis-driven research in biology obsolete. Others say that such 'investigation' is no longer science.

We suggest that some middle-ground will probably win out and both forms of inquiry will prove useful in answering important biological questions. What is your opinion?

Posted by Daniel Evanko at 01:00 PM | Permalink | Comments (2) | TrackBacks (0)

In our March Editorial we discuss the need for improved communication between scientists and the public via dedicated science media centers as well as nontraditional personal blogs.

In an effort to do our part in improving lines of communication we are working to transition methagora from a commenting forum to a more traditional blog. We intend to use the site to discuss some of the papers we publish, provide information on upcoming conferences we will be attending (and hopefully reports on these conferences), as well as anything else we think would be useful to our readers. Keep an eye out for our upcoming entry on the most downloaded articles from our January issue.

This is a work in progress and we welcome feedback from our readers on what information you would like to see here.

Posted by Daniel Evanko at 10:01 AM | Permalink | Comments (4) | TrackBacks (0)

The February Editorial in Nature Methods discusses the challenges raised by the dvelopment of large-scale centralized biobanks and calls for scientists to engage the public in a conversation on biobanks as a groundwork for lawmakers to provide a legal framework that protects public and individual interests. Share your thoughts on this important issue.

Posted by Daniel Evanko at 10:05 AM | Permalink | Comments (1) | TrackBacks (0)

In the spirit of the upcoming 2008 Olympic Games in Beijing an Editorial in the August issue of Nature Methods discusses the use of organized competition for evaluating algorithm performance. Such competitions, or "collaborative experiments", have become very popular in some large communities.

We believe similar competitions would also be helpful for smaller communities. What do you think? Is it more trouble than it is worth or would it be a valuable way of pushing algorithm performance to new heights?

Posted by Daniel Evanko at 01:00 PM | Permalink | Comments (2) | TrackBacks (0)

How do you handle terabytes of data? That is a question that more and more investigators must face, on a weekly basis.

Are you one of them? Light-sheet fluorescence imaging, for example, generates so much data in each experimental run that handling and storing the raw data is a challenge. Next-generation sequencing is another, much more ubiquitous, case.

Read the July issue editorial “Byte-ing off more than you can chew” and let us know about your own experience, problems and practical (or impractical) solutions.

Posted by Veronique Kiermer at 01:00 PM | Permalink | Comments (1) | TrackBacks (0)

In the May Editorial, Nature Methods' Editors list their top ten pet peeves about conference presentations. Check out the list and add your tips!

Posted by Veronique Kiermer at 01:00 PM | Permalink | Comments (2) | TrackBacks (0)

Sooner or later, any scientist is likely to be confronted by a supporter of “intelligent design” (ID), or questioned by a student, friend or neighbor intrigued by the concept of ID. Check out our idea of a response here and share your thoughts on what yours would be.

Posted by Nicole Rusk at 02:55 PM | Permalink | Comments (3) | TrackBacks (0)

The Global Theme Issue on Poverty and Human Development went live today: 235 scientific journals coordinated the publication of articles specifically addressing issues related to human condition in poverty-stricken areas. This initiative was spearheaded by the Council of Science Editors and the full list of articles can be found on their web site. A special event was hosted at the US NIH on the occasion of the coordinated publication.

Continue reading "Research in situ, where it is most needed. " »

Posted by Veronique Kiermer at 10:37 PM | Permalink | Comments (0) | TrackBacks (0)

The process of getting a manuscript published can be a long and sometimes convoluted one. The more transparent it is, however, the more likely that members of the scientific community will be able to negotiate it to their benefit. In our September editorial, we provide a brief primer on key steps in the process, especially those where problems are likely to be encountered.

Posted by Natalie De Souza at 05:01 PM | Permalink | Comments (0) | TrackBacks (0)

A bill designed to prohibit discrimination based on genetic information in terms of health insurance and employment is awaiting a vote in the US Senate. There have been several similar but ultimately unsuccessful legislative attempts over the past 12 years. It is crucial that this bill be enacted into law to address a public fear likely to limit patient access to predictive genetic testing and to discourage participation in genetic research.

Continue reading "No faulty-gene carrier need apply" »

Posted by Veronique Kiermer at 02:00 PM | Permalink | Comments (0) | TrackBacks (0)

In an editorial in the July issue, we suggest some recent popular science books that would make a nice summer read and hope that summer will not be the end of it. To keep you going, here are an extended list of older books, including some of our favorites and some of the genre classics. The list was assembled with the kind advice of editors, scientists and science writers.

Continue reading "Staff picks" »

Posted by Veronique Kiermer at 08:31 AM | Permalink | Comments (0) | TrackBacks (0)

For geneticists working on model organisms, the job is all about linking genotype and phenotype. But nowadays, these researchers are facing a historical reversal in terms of experimental limitations. As more microarrays and other genomic tools become available—and hopefully increasingly affordable—the genotyping part of the problem, which traditionally has been most time-consuming, is not that complicated anymore. The real bottleneck is now phenotyping.

In an Editorial in Nature Methods June issue, we argue that this realization should be a call to arms for engineers.

While we think there is a crucial need to mobilize engineers to help develop assays and instrumentation for high-throughput phenotyping of model organisms, this task is not without obstacles. The Editorial starts exploring ways to make this work. What do geneticists and engineers among you think?

Posted by Veronique Kiermer at 02:00 PM | Permalink | Comments (0) | TrackBacks (0)

The discussion topics below and some insightful comments illustrate how a commenting forum like this one can empower readers, allowing them to participate in important discussions of direct interest to their work. But readers are slow to seize this opportunity. We have taken a look at this attitude in a recent editorial.

Let us know what you think and how we can make this forum better for you.

Posted by Veronique Kiermer at 09:28 AM | Permalink | Comments (1) | TrackBacks (0)