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Most coders come to bioinformatics by one of two routes. They’re either biologists skilled in programming, or programmers with an interest in biology. Mike Goodstadt, the programmer behind the genome-visualization tool TADkit, took a different approach.
In the early-to-mid 1990s, Goodstadt was a student at the University of Bath in the UK. His course of study: Architecture. Continue reading
It’s been nearly a decade since Eric Welsh first noticed some weirdness with Microsoft Excel. A senior staff scientist in the Cancer Informatics Core at the H. Lee Moffitt Cancer Center and Research Institute in Tampa, Florida, Welsh was using Microsoft’s venerable spreadsheet application to view mouse and human gene expression data, the better to sort and understand the numbers. But a quick glance revealed the import hadn’t gone exactly as planned. “Excel would screw them up every time,” he says.
How so? When data are imported into Excel, the program works hard to figure out what kind of value each cell holds. Most of the time, Excel is smart enough to do that correctly, and values like ‘BRCA1’ and ‘12345’ are converted into text and integers, as expected. But “Excel is a little too smart for its own good,” Welsh says. If a cell reads “SEPT7,” the program assumes the author meant to write a date, and converts it automatically. It also sometimes translates what appear be numbers in scientific notation – say, ‘2310009E13’ – into actual scientific notation (‘2.31E+13’). The problem is, those two terms are neither dates nor numbers – they are proper names, scientifically speaking: gene names, sample identifiers or accession numbers. And by autoconverting them, those names are lost, or at least, obscured.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-80
Beginning this week, we will take a peek into the lives of Indian postdocs working in foreign labs. Our blog series ‘Away from home’ will feature one postdoc every Tuesday recounting his/her experience of working in a foreign lab, the triumphs and challenges, the culture factor, tips for Indian postdocs headed abroad and what he/she misses most about India.
Kangkan Halder
Teeing off the series for us is Kangkan Halder, who completed his doctoral thesis at the Institute of Genomics & Integrative Biology (IGIB), New Delhi and is currently a post-doctoral fellow at the Applied Synthetic Biology Group at the University of Göttingen, Germany.
Science and I
I am not sure what really got me interested in science, but I guess I was plain curious about things. I also liked the idea that in science there is a specific answer/reason for a specific question/observation. On the other hand, for any generalization there is always an exception too! And I was really curious to know these exceptions.
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