One thing's certain at the Keystone Symposia on linkurl:Structural Genomics;http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=817 and linkurl:Frontiers in Structural Biology;http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=816 running this week in Keystone, Colorado: there's some seriously big science going on in the world of structural biology. Aled Edwards of the University of Toronto rattled off the program goals of the linkurl:Structural Genomics Consor

A few days ago I blogged on linkurl:a new fluorescent protein;http://www.the-scientist.com/blog/display/22976/ called KillerRed. Upon irradiation with green light KillerRed produces reactive oxygen species in sufficient quantities to kill both prokaryotic and eukaryotic cells. The authors suggest several potential applications, but I?ve come up with another: hypoxia research. Before I joined __The Scientist__ I was a postdoc in Celeste Simon's lab at the University of Pennsylvania. Simon works

A fundamental goal of systems biology is to define a biological system precisely, such that it becomes possible to predict the outcome of perturbing that system. Yesterday (Jan. 22) a team of researchers from German drug discovery firm Cellzome and the European Molecular Biology Laboratory linkurl:reported in __Nature__;http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature04532.html a significant step toward the creation of such models, at least in budding yeast. Giulio Superti-Furga a

Poking around on the linkurl:iSpecies blog;http://ispecies.blogspot.com/2006/01/antweb-google-earth-map.html today, I found a comment alerting readers to linkurl:an interesting little tool;http://www.practicalfishkeeping.co.uk/pfk/pages/DEVmapform.php on the online version of __Practical Fishkeeping__, "the UK's best-selling aquarium magazine." Fish Mapper is an applet that plots fish distribution data, culled from an online service called linkurl:FishBase;http://www.Fishbase.org , us

Yesterday (Jan. 17) the Wellcome Trust Sanger Institute linkurl:announced;http://www.sanger.ac.uk/Info/Press/2006/060117.shtml that its linkurl:World Trace Archive database;http://trace.ensembl.org had just crossed the 1 billion sequence mark. The Trace Archive is a collection of sequence reads, traces, and metrics from the world's sequencing facilities. It measures some 22 Terabytes in size and is doubling every 10 months, according to the press release. "To grasp how much data is in the

This month?s __Nature Biotechnology__ linkurl:includes an article;http://www.nature.com/nbt/journal/v24/n1/abs/nbt1175.html from Sergey Lukyanov that elevates fluorescent proteins from cool to killer. Lukyanov, of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, and colleagues report the isolation of a GFP variant called KillerRed that acts as a photosensitizer. Photosensitizers produce reactive oxygen species upon stimulation with light; Killer

Researchers have, since 1988, been searching for a so-called "universal nucleant," that is, a material that will nucleate crystal formation, much as a grain of sand nucleates the formation of a pearl. Buried in the biophysics section of PNAS's January 6 Early Edition is linkurl:a somewhat esoteric paper;http://www.pnas.org/cgi/content/abstract/0504860102v1 that may just end this search -- and open one of structural biology's most persistent bottlenecks, generating high-quality crysta

I found two cool new tools today. The first, via Sourceforge, is PuMA, a standalone Java front-end to PubMed. PuMA (currently at version 1.0alpha) allows you to view bibliographic search results and abstracts in the same window, visually construct complex Boolean queries, and export data to EndNote, Reference Manager, ProCite, and BibTex. It also offers keyword highlighting, links to Google and Google Scholar (for instance, to find articles citing another's work), and an intuitive user interface

A research team at Los Alamos National Laboratory has topped a world record for biological simulations, and given us a taste of reducto ad absurdum. As reported in the Nov. 1 issue of PNAS the LANL team, led by Kevin Sanbonmatsu, used 768 of the 8,192 CPUs in LANL's ASCI Q supercomputer to model the motion of 2.64 million atoms in a ribosome complex -- 250,000 in the ribosome itself, and most of the rest from water molecules. The processors chugged away for some 260 days, completing 20 milli

Chris Mooney's "The Republican War on Science" showed up on my desk recently. The book traces the rise of the Republican Party's split with science, from its roots in the supersonic transport debate in the Nixon administration, to George W. Bush's assault on science today, covering science issues from Reagan's "Star Wars" initiative to "intelligent design," global warming to stem cells.From what I read Mooney seems to come across as a bit of a zealot. In the first chapter, for instance, he w

The latest e-TOC from the journal Bioinformatics contains an application note on a really cool tool. ProTag is a Microsoft Office extension that uses biological name and markup services called ProThesaurus and LiMB to find protein names and database identifiers in Word, Excel, and Powerpoint documents. From there, you can perform a range of actions on that text, all without ever leaving the Office. So, for instance, if you type the phrase ?TIM4_HUMAN is the SwissProt identifier for tissu

Microarray data quality is an issue that has been covered extensively in The Scientist (see, for instance, here and here). The basic issue is this: how reliable are the sometimes-subtle changes in gene expression levels these experiments yield, and how reproducible are they.The External RNA Controls Consortium, an ad-hoc group with approximately 70 members from private, public, and academic organizations formed in 2003, is one of several groups working to address these questions. The Consort