Naming scientific software

Posted on 30 Jul 2009 by Daniel Evanko

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.

Method of the Year 2009 voting begins

Posted on 30 Jul 2009 by Daniel Evanko

Two years ago we decided we wanted to do something each year to celebrate the importance of new methodological developments in biological research, and the people who bring them to fruition. In 2007, it was clear that next-generation sequencing was going to have a profound impact on scientific research. Therefore, it was an obvious first choice when we decided to start selecting a ‘Method of the Year’.

Last year we invited our readers to help us in the selection of the Method of the Year 2008 by nominating and voting for their choice. While participation was good, it wasn’t high enough to have much impact on our choice. This year we are starting voting a month earlier and are hopeful that the level of participation will be substantially higher.

We also want to clarify that we are not asking people to nominate and vote for papers published in Nature Methods. Although anyone who wants to nominate a Nature Methods paper is welcome to do so, we hope that readers will consider the broader universe of biological research methods.

It is quite likely that our choice will not be a method represented by a single paper but rather a class of methods like next-generation sequencing or super-resolution imaging. But readers are welcome to pick a single paper that represents a broader methodological advance they want to nominate and explain their choice to other readers.

We have already seeded the voting with our Methods to Watch from the last two years. Maybe one of them will now be ready to be declared Method of the Year.

As always, we welcome your feedback and encourage you to vote for the method you think deserves to be declared the Method of the Year 2009 and encourage your colleagues to do so as well. Just go to https://www.nature.com/nmeth/votemoy2009 and start voting!

Top downloads for June ’09

Posted on 12 Jul 2009 by Daniel Evanko

Here are the top downloads for June. Due to lack of time I have to forego any comments this month but I’ve posted the rankings of the five most popular papers published in our June issue based on PDF downloads during June.

Top 5 research papers published in the June issue

1. Predicting microRNA targets and functions: traps for the unwary

2. Automated unrestricted multigene recombineering for multiprotein complex production

3. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

4. Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster

5. High-throughput ethomics in large groups of Drosophila

There has been quite a reshuffling of the ten most popular papers published prior to our June issue and downloaded during June. Part of this movement may be due to the fact that beginning this month I have decided to use the number of successfully downloaded PDFs rather than combined PDF and HTML views but I think most of the explanation is the high quality of the papers published in our May issue which have displaced some of the older papers.

Top 10 research papers published prior to the June issue

1. Mapping and quantifying mammalian transcriptomes by RNA-Seq

2. mRNA-Seq whole-transcriptome analysis of a single cell

3. Universal sample preparation method for proteome analysis

4. Isolation of human iPS cells using EOS lentiviral vectors to select for pluripotency

5. Super-resolution video microscopy of live cells by structured illumination

6. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon

7. Stem cell transcriptome profiling via massive-scale mRNA sequencing

8. Genetically encoded fluorescent indicator for intracellular hydrogen peroxide

9. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

10. Enzymatic assembly of DNA molecules up to several hundred kilobases

PRIDE Converter – A new tool for proteomics

Posted on 10 Jul 2009 by Veronique Kiermer

The administrators of the EBI proteomics repository PRIDE have just announced, in the July issue of Nature Biotechnology, the availability of a software tool to facilitate data deposition.

According to Lennart Martens and co-authors, the new tool, PRIDE Converter, “makes it straightforward to submit proteomics data to PRIDE from most common data formats.” This comes handy.

Depositing proteomics data into a structured public repository is a very worthwhile effort—one that Nature Biotechnology, Nature Methods, and other Nature journals strongly encourage. To date, however, the problem has been that in some cases, depositing data remained an effort.

Things could get particularly challenging if you happened to have large datasets in instrument-specific formats. Converting these into the XML-based format needed for data submission required time and informatics skills. Apparently, now, PRIDE Converter does it for you.

Proteomics researchers need effective ways of sharing data. Submission of data to public repositories upon publication should become as automatic in proteomics as it is in some other fields. But realistically, this can only happen if a good infrastructure of databases is in place—it is—and if the submission process is not an undue burden on the researchers.

Kudos to PRIDE, thus, for taking this step in the right direction and for demonstrating a willingness to work with researchers to facilitate submission. It is up to proteomics researchers now, to make use of the tool, and work with its authors to continuously improve it as the field, and their needs, evolve.

Recent methods papers from the literature

Posted on 08 Jul 2009 by Allison Doerr

Our July issue went live last week, and as always, it includes our popular Research Highlights section. Here is a list of some interesting methods papers we considered (which were published over the last month or two) but were not able, because of space reasons, to cover in the journal.

Metastable Pluripotent States in NOD-Mouse-Derived ESCs

Cell Stem Cell 4, 513-524 (2009)

A Small Molecule Primes Embryonic Stem Cells for Differentiation

Cell Stem Cell 4, 416-426 (2009)

Reprogramming of murine fibroblasts to induced pluripotent stem cells with chemical complementation of Klf4

PNAS 106, 8912-8917 (2009)

Diversity and Complexity in DNA Recognition by Transcription Factors

Science 324, 1720-1723 (2009)

Efficient siRNA delivery into primary cells by a peptide transduction domain–dsRNA binding domain fusion protein

Nature Biotechnology 27, 567-571 (2009)

Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

JACS 131, 7320-7326 (2009)