Prettier Code

August 27, 2012

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Research code can be messy stuff and tweaked on the fly to examine different hypotheses, writes Iddo Friedberg at Byte Size Biology. "Research coding is not done with the purpose of being robust, or reusable, or long-lived in development and versioning repositories," he says. "Upgrades are not provided and the product, such as it is, is definitely not user-friendly for public consumption." However, as a Twitter conversation Friedberg had points out, the code could have bugs or errors that affect results. Friedberg notes that the Bioinformatic Testing Consortium, of which he is part, aims to test such code. "A great idea, and if taken up by journals, having your BTC-approved code accompanying your paper would go a long way to validating the science presented in your research article," he says.

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Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

Data presented in this webinar illustrates the value of live cell analysis at the single-cell level to identify differences in expression levels across populations of cells. The cells remain intact for downstream analysis. Our experts also discuss the use of SmartFlare RNA detection probes for the direct quantification of circulating miRNAs with rapid processing of blood plasma/serum, which is done without the use of enzymes. Using circulating miRNAs with established roles in cancer and quality control, we can accurately detect these miRNAs in plasma using a microplate fluorometer within an hour after plasma preparation.

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Optimization of NGS Library Preparation: Low Inputs and Fast, Streamlined Workflows

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Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.

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Bernd Bodenmiller

Group Leader
University of Zurich

Single-Cell Proteomics

University of Zurich researcher Bernd Bodenmiller studies single-cell signaling with a technology almost as newly minted as his lab.

Bodenmiller launched his lab in February, and three months later, in May, he installed the instrument that has become key to his work — DVS Sciences' CyTOF mass cytometer, a new take on flow cytometry that lets scientists measure dozens of targets at once in single cells.

During his PhD work, Bodenmiller focused on the analysis of protein phosphorylation and cellular signaling. As he was wrapping up his thesis, though, he says he realized that "if you want to study signaling in disease, then you need the ability to study signaling on a single-cell level."
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Papers of Note

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us
El Baidouri, Diancourt, et al. PLOS Neglected Tropical Diseases

Through a multilocus sequence analysis of 222 African and Eurasian Leishmania isolates, French researchers identified seven genetic clusters of Leishmania in the regions tested. For the most part, those clusters corresponded to existing Leishmania classification schemes, the study authors note, though their analysis suggests genetic distinctions are somewhat hazier for three Leishmania species implicated in visceral forms of leishmaniasis. "Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles," they say, "they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago."

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna
Nakamura, Mori, et al. Proceedings of the National Academy of Sciences

AJapanese team describes findings from a genome sequencing study focused on the Pacific bluefin tuna, Thunnus orientalis. An analysis of the genome revealed more than 26,400 predicted protein-coding genes, including genes coding for rhodopsin and opsin pigments poised to pick up blue, green, red, and UV light. Within genes coding for the color-sensing proteins, researchers found substitutions and duplications suspected of helping bluefish tuna differentiate between blue and green. If so, that could confer an evolutionary advantage in the fish's ocean environment, they say, perhaps explaining some aspects of the tuna's predatory proficiency.
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Direct-to-consumer genetic testing firm 23andMe has appointed Andy Page as its president, a newly created post. Page, who has served as a member of 23andMe's board of directors for the past year, will report to CEO and co-founder Anne Wojcicki. He was previously president of the Gilt Groupe, an online luxury shopping website, and chief operating and financial officer at PlayPhone.

The Ludwig Institute for Cancer Research has appointed David Lane to be its new scientific director, effective June 1. He succeeds Andrew Simpson, who was scientific director for five years, from 2007 to 2012. Lane is chief scientist at Singapore's Agency for Science, Technology, and Research, and he will retain that post in addition to his new role at Ludwig.

Kevin Hrusovsky is resigning his post at PerkinElmer as senior VP and president of the Life Science and Technology division. Hrusovsky will serve as a consultant to the company for up to one year, beginning in June. He joined PerkinElmer through the company's acquisition of Caliper Life Sciences, where he was CEO and president.
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An international research team has uncovered unexpected genetic diversity in the miniscule marine algae Emiliania huxleyi, a species now known to have the type of variable 'pan genome' previously described in some bacterial species. They detected an array of genes and repetitive sequences that are present in some E. huxleyi strains but not in others, varying with each strain's habitat, physical features, and metabolic capabilities, among others.
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The US investment in the Human Genome Project and the ensuing federal funding for genome science has reaped massive economic benefits, according to a new study from Battelle. It found that genomics-related fields from biomedicine to energy and agriculture have had a $965 billion impact on the US economy, stemming from a total of $14.5 billion in federal investments between 1988 and 2012. Genomics-related funding has yielded a $65 return on every $1 invested.
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GenomeWebinar: Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

GenomeWeb and EMD Millipore invite you to view an archived webinar discussing new approaches to detect RNA at the single-cell level as well as new probes for the direct quantification of circulating miRNAs. In this free online seminar, recorded April 25, 2013, our expert panel shares protocols for improved RNA and miRNA detection.

On-demand recording available here.

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