Articles by Sam Jaffe

Angela Howard was concerned when her infant daughter stopped crying, despite repeated jabs with an IV needle.

Despite lack of life on Saturn's moon, astrobiologists could gain much from mission

When scientists make long-term research plans, they must try to anticipate how emerging technologies will influence their work in the coming years.

Microarrays are wonderful tools for seeing global patterns of gene expression under different conditions.

Few research tasks are as time-consuming and tedious as scouring the scientific literature. The searcher might need only one nugget of information, yet it can take hours or days to slog through hundreds of papers before that one fact is found. Now, a new open-source tool called Textpresso http://www.textpresso.org can find a single fact just by typing in a quick search entry.Paul Sternberg's lab at the California Institute of Technology designed Textpresso to organize papers on Caenorhabditis el

Roland Siezen and colleagues at the University of Nijmegen, the Netherlands, have created a software tool that's long overdue. Most researchers in the eukaryotic model organism community have genome browsers capable of integrating and overlaying various datasets to produce annotated chromosome maps. Microbiologists, though, have been largely out of luck.Now the playing field has been leveled a bit. Microbial Genome Viewer (MGV; http://cmbipc49.cmbi.kun.nl/genome) is a free, open-source program t

Courtesy of Filippo RusconiWhile a graduate student, Filippo Rusconi couldn't come up with the money to pay for a Microsoft developer's license to continue work on his mass spectrometry program. So instead he rewrote the whole program in GNU/Linux. It turned out to be the best thing that happened to him, he says. "It allowed me to make the program a thousand times more powerful."The program, now called GNU polyxmass http://www.polyxmass.org is a complete software suite for mass spectrometrists t

Courtesy of IBMA new effort to unify the naming conventions of biological data is now underway in labs and companies throughout the world. The Life Science Identifier (LSID) Resolution Protocol Project consists of two software programs and a set of naming standards http://www.ibm.com/developerworks/oss/lsid.The first program is a server application called LSID Authority, which allows database and Web-site managers to identify their data with LSID URNs (uniform resource names, similar to URLs). T

For a 30-year-old experimental method, gel electrophoresis remains popular. Originally devised as a method to extract nucleic acids from solution, it has evolved into a method for the analysis of everything from protein expression to matching RNA expression to proteins. "When we opened this facility three years ago, some people told me that in three years you won't do gel electrophoresis any more, so why invest in the equipment?" says Thomas Franz, head of the proteomics core facility at the Eur

Adecade-long war over genetically modified mice still rages. In 1994, Klaus Rajewsky's laboratory at the University of Cologne in Germany created the first transgenic conditional knockout mouse.1 With this mouse, researchers could turn on a genetic mutation at a specific period of development in a specific type of cell. Rajewsky assumed that his mouse would soon be used in labs throughout the world. Simply pleased with his research success, he never considered applying for a patent on a mouse. "

For decades, the behavioral sciences have been at a dramatic disadvantage to the hard sciences. When a biologist hypothesizes that the addition of a particular ligand to a cell will cause a certain gene to turn on and thus produce a certain protein, all she has to do is to introduce the enzyme and then test for the protein. If it's there, she publishes a paper; if it's not, she quietly discards the work.The psychologist has a much steeper hill to climb. Let's say he's trying to prove his hypothe

Reanalysis of data shows that many cases of intussusception were unrelated to vaccine

BRINGING ON THE NEXT ICE AGE?Dee Breger, Drexel UniversityAssumptions that tiny diatoms such as the ones shown above could fix carbon from the air and sink it to the bottom of the ocean have been hard to prove.The US Department of Energy has taken an interest in carbon sequestration, but a grand scheme to induce thick blooms of carbon-fixing algae has yet to bear fruit in early studies. The DOE directs a large share of its global warming budget to carbon-sequestration research, drawing on biolog

Courtesy of CellwareThere are more than 60 in silico modeling programs available to systems biologists, including expensive proprietary packages and niche open-source projects. Most of them, though, rely on one kind of algorithm to calculate a model.That's why Pawan Kumar Dhar, a senior research scientist at the Bioinformatics Institute in Singapore, designed Cellware http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp. "In gene expression, you would usually use deterministic algorithms

Every resource carried onto a manned spaceship is precious, because it costs hundreds of dollars to lift each pound of material past Earth's surly bonds. Now that NASA is in the process of planning a trip to Mars that might take up to two years, no type of recycling can be overlooked. One thing that can provide three basic raw materials (water, energy, and fertilizer) needed for a long space journey: human waste.Most methods of recycling organic waste involve the production of methane, a flammab