Round 2.3: Making Connections
For our next exercise, we’re going to skip ahead to Chapter 4 of How Learning Works (which is about integrating skills and knowing when to apply them) and Chapter 5 (which discusses goal-directed...
View ArticleRound 2.3 Making Connections with DNA sequencing
My research deals with DNA sequencing of environmental communities. A major barrier to working with this type of data is that the current sequencing technology we use outputs numerous short lengths of...
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Extracting data using regular expressions, the shell, and version control
Research in my lab often requires acquiring and cleaning up other people’s data. One of the most difficult forms of data to work with is data stored in PDFs. On a recent project a graduate student was...
View ArticleRound 2.3: fitting non-linear functions to psychophysical data
Not quite what we were supposed to do: I started out trying and then before I knew what happened, there it was. I was never very good at following instructions.
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Round 2.3: combining shell commands and R
Adina nicely introduced the concept of DNA sequencing in her round 2.3 post. The sequencing data that she describes comes from a platform that generates pieces of sequence (called ‘reads’) up to a few...
View ArticleRound 2.3 – manipulating sequence data with python
A while ago a colleague of mine asked me for a bit of help. He knew I often work with sequencing data, and he hoped I could assist him with sorting out his sequencing sets. What he wanted help with was...
View ArticleMy Experience with SVN + SQLite + Python
We had a project where we where collecting metadata (data about data) for a filesystem of astronomy images. The File system was growing daily and soon we had ~22k images. The metadata (target,...
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