Bradford Condon PhD

Bioinformatics, Web & Mobile Development


science

I’m excited to announce that my wife Dr. Ellen Crocker and I will be teaching a workshop at the Floracliff Nature Sanctuary on Friday and Saturday, October 14th-15th 2016.  I’m particularly proud to partner with Floracliff: it’s a beautiful nature preserve with very cool educational opportunities available to the public.  Ellen has taken Rob Paratley’s fern workshop and she said it was fantastic.

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Sometimes, you have a task where the goal is to remove a certain phrase, set of characters, or trailing characters within a file. This happens all the time working with FASTA files. For whatever reason, the header description might be longer than you like. Some phylogenetics programs, for example, have a character limit on headers. Failure to fix this on your own can result in clipped headers, which in turn can result in non-unique headers and failed scripts.

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Phyloseq is a fantastic R package that really helped me get started in R.  If you need to process your metagenomic data but lack the experience in statistics/R to use, say, the ecology stats R package VEGAN, I highly recommend giving Phyloseq a try.  Running through the vignettes will produce great heatmaps, taxonomy plots, and PCA/NMDS plots.

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When I taught a science for non-science majors at Cornell University, my favorite lecture was on science in the popular media. My learning objective was straight forward: I wanted students to pick up a newspaper, flip to the science section, and detect bullshit. This is such an important life skill because at this point in time, blogs, newspapers, and magazines print unscientific bullshit. They do it because it sells. I have never seen an article so neatly package all of the problems that lead to this state of affairs than John Bohannon's recent "Chocolate Diet" charade. Read the full post...

Last year, I wrote about using Evernote as my digital lab notebook.  With the release of Findings, a new digital notebook software from the people who created my favorite reference management software Papers, I thought I would reflect on my digital notebook needs.

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This morning I was delighted to come across the IMA Fungus journal.  Put out by the International Mycological Association , the journal title (which primarily publishes species announcements and descriptions) playfully introduces each organism with a friendly “Hello, I’m a fungus!”  The truth is, scientific literature is seldom so fun and informal.

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Back in September last year, I explored some possibilities that the “Stem Cell burger” opened up.  Perhaps the most far-fetched idea I had was to produce meat from cloned celebrity stem cells.

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In the past, I’ve written about the importance of setting up custom newsfeeds for current publications in your field, and using Citeulike to share references.  While these tools can be useful for discovering and archiving content, they are not ideal for sharing and disseminating it.  Gathering content and distilling it for others is an art: the art of content curation.

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What does it mean to be a scientist?  I present to you some overly poetic thoughts on the topic.

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An article posted on the Scientific American blog caught my attention recently.  Researchers have discovered the existence of a new organelle, the tannosome, in plants.  It is this organelle that produces tannins, of great interest to wine lovers.  The scientific article in question, posted to my scoop.it, was officially published in the Annals of Botany on September 25th 2013, but it barely created a ripple in the news cycle.  Why not?

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I am  writing a short piece on the Stem Cell Burger which was unveiled early last month.  The Cultured Beef website is eager to point out the many benefits this technology could have for global research usage and animal ethics.  Opponents are just as quick to point out the possibility of unknown side-effects.

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When I first started graduate school, I kept an old-fashioned notebook.  A 4×4 quad ruled Roaring Spring Lab Notebook.

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I was reading this Nature article by Kim Gardiner and Hugh Kearns on snack writing.  Their argument is that scientists who write in a small, fixed window, 45 minutes a day, every day, write more than “block writers” who blackout entire days for writing.

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Dropbox is simple and intuitive.  Make a folder on your computer that is automatically backed up to a cloud storage account.  Suddenly, the files you work on and the data you access syncs across devices, at home and at work.  Plus, you can dropbox folders with others.

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RSS (rich site summary, or, really simple syndication) is an invaluable tool for all academics.  If you ever wish it was easier to stay up the current academic literature, then this is tool for you.

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Before you can do good science, you must read good science.   A lot of it.  The good, the bad.

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I’m pretty sure I have too many gadgets for managing my academic references.  I’d surely be better off if I spent more time reading the literature, and less time setting up new accounts that I’ll neglect (this blog being a perfect case in point).

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