Short sentences (prose, not prison)
Posted in Tips
PLoS One requires full data release with publication
Posted in Uncategorized
authors must make all data publicly available, without restriction, immediately upon publication of the article
Examples could include spreadsheets of original measurements (of cells, of fluorescent intensity, of respiratory volume), large datasets such as next-generation sequence…
ACQ4: A Python-based open source system for neurophysiology
Posted in Software
Luke Campagnola, Megan Kratz, and Paul Manis recently published their in-house software for neurophysiology experiments. It’s an extensive set of tools, including multiphoton imaging, photostimulation mapping, image mosaic construction, electrophysiology, and more.
Website: acq4.org
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More resources
Posted in Tips
André Maia Chagas recently pointed us towards his blog, Open Neuroscience. It turned us on to Sparkfun’s educational section. It’s very extensive and well curated.
By the way, Sparkfun also has education discount…
Box plots vs. bar charts
Posted in Software
Nature Methods has a special on box plots, and in particular, the web app BoxPlotR.
Box plots are great. However, the conventions for box plots are not completely uniform (see below), and that…
Damage thresholds and Ti:Sapph lasers
Posted in Hardware
Recently, a moderately expensive optical element got fried at Labrigger. During the postmortem, we revisited our power and energy calculations, and our LIDT (laser intensity damage threshold) calculations.
LIDT calculations remind me of radiation-health…
Processing 2
Posted in Software
One of the first posts in this blog was on Processing. Processing is a programming language with an integrated development environment that is specialized for simplicity– ease of learning and…
Why is anonymity important?
Posted in Uncategorized
Following up on these recent posts… here’s a twitter discussion from a couple of weeks ago…
F1000’s Caeser Berrios says that people who want to participate anonymously in post-publication peer…
Lazy Scholar Chrome plugin for searching for papers
Posted in Software
Colby Vorland coded this Chrome plugin called Lazy Scholar to make it easier to find full text versions of papers. It basically cross references a bunch of databases for you, to find information…
Searching for post-publication peer review, and a new use thereof
Posted in Uncategorized
PubMed Commons has a search argument you can use to find articles with comments:
has_user_comments
You can click that link to try it yourself.
As of this writing, there are about 650 comments on all of PubMed Commons. I don’t know how this compares…
Giant Brain Discussion
Posted in Uncategorized
Carson Chow’s blog announced:
There is an epic discussion on the Connectionist mailing list right now.
He followed up with his two cents entitled “(Lack of) Progress in neuroscience”.
It’s an on-going, vibrant discussion on…
Defamation, science, and free speech
Posted in Uncategorized
In the US, the First Amendment’s guarantee of freedom of speech protects many insults that can be lobbed at a person. However, a line is crossed into defamation, a civil or criminal…
“well, damn if Jack doesn’t have some good points here”
Posted in Tips
Please enjoy this story from Mistress of the Animals about how her old mentor would keep all of his reviews– in the days of typewriters– and then compare new reviews to…
Thorlabs’ 0.26 GB catalog
Posted in Uncategorized
Thorlabs released a ridiculously sized (264 MB) PDF catalog for their life sciences imaging. Despite the size, I recommend downloading it and checking it out. There are several items and lots of product details…