So, you’ve managed to launch Galaxy on Amazon Web Services EC2, and now you’re trying to upload all of your RNA-seq files to run TopHat and Cufflinks. Great! But it’s taking 5 (five!) days to transfer your data. That’s going to cost a ton of money if you keep your Galaxy instance running on EC2 the entire time. Luckily for you there is a better way. Continue reading
In a previous post I played around with Amazon Glacier, using a tool called glacierFreezer. Since then, I’ve wanted to automate backups of my Time Machine archives, as well as my photos and home directories. Looking around for more current Glacier interfaces I noticed a project called glacier-cmd which looks promising. The core utilities are written in Python, and provide means to upload, download, and query Glacier vaults.
Last year it was just a rumor, but yesterday Retraction Watch covered an official retraction from a neuroscience lab at Hopkins. The retraction notice:
Our paper reported an analysis of a mouse genetic model that deletes the C terminus of Shank3 to mimic human mutations that cause autism spectrum disorder. Figure panels for several polyubiquitination assays were improperly assembled, leading to multiple repetitions of bands in western blots of the lysates. These errors did not affect the quantitative analysis of polyubiquitination because this analysis was performed as described and was not dependent on representative western blot images. In light of the figure preparation issues, we feel that the most responsible course of action is to retract the paper. We sincerely apologize to the scientific community for any misunderstanding that these errors may have caused.
Well done for preventing the spread of misinformation. It must hurt to issue a retraction, but it sounds like the conclusions still stand regardless of the “improper assembly” of the representative Western blots. When are we going to learn to stop trusting Western blots in papers?
I really appreciate all the feedback. You’ve made my day and my new year!
The Raspberry Pi is a fairly powerful $25 single-board computer targeted toward the educational market, though just because it’s for kids doesn’t mean it’s not fun for adults. I’ve been wanting to buy a Pi for a while now, but couldn’t justify purchasing hardware I have no use for – that is, until I saw this blog post detailing how to use the Pi as an Apple Airplay receiver. This is perfect. Let’s get started turning our little computer into a single-purpose appliance.
I recently bought a really fun mini RC helicopter. It’s made in China by WL Toys, and it packs lots of technology into a ready to fly kit. Flying it has been a blast, but the manufacturing quality control leaves something to be desired. The remote control has a small piece of something rattling around in it, which doesn’t affect the function at all. The battery charger is supposed to charge two of the Li-polymer batteries simultaneously, but it seems like mine only has one working port:
Dave Brubeck, the composer and pianist that exposed many decades of young people to jazz, died yesterday at the age of 91. He literally brought jazz to college by integrating classical European composition elements such as alternating time signatures and introspective chord progressions. Some people, including my favorite music professor Michael Budds, hinted that Brubeck couldn’t swing like other contemporary jazz innovators. I think he just swung more subtly. He had to, since the styles of music he integrated were viewed as diametrically opposed in nature. Along with other visionary composers such as Duke Ellington, Brubeck left more than the legacy of his songbooks and great recorded performances; he pushed the concept of jazz as art and intellectual stimulus into homes worldwide. Dave Brubeck (along with Paul Desmond, Joe Morello, and Eugene Wright) introduced me to jazz that’s not “old-timey” – not a caricature of another decade. His death will surely not stop future generations of young people from enjoying this great American art form. Rest in peace.
PS: This morning (Dec 10) Tom Hall aired his thoughts about Brubeck as well as a three year old interview between the two.
Tomorrow, Baltimore’s newest (only?) “bio-space” is hosting a hands-on synthetic biology workshop. BUGSS is not a group I’m associated with, but that may change soon, because it looks like they are having tons of fun. With a bit of lab equipment and some e.coli, these guys are hosting some 18+ and all-ages workshops to expose more people to actual molecular biology experiments. I wish this type of thing existed when I was in high-school.
Recently I gave a presentation about Galaxy, and as part of the presentation I walked about 30 people through setting up a Galaxy cluster through Amazon Web Services (AWS). The AWS setup took most of an hour, and moving 30 people through each step was painful. From pain comes prosperity (apparently), because today I stumbled on a link from the main Galaxy public server that allows a user to automatically initialize a Galaxy cluster through AWS! Where were you last month? Anyway, I’ve updated the presentation with a link to the site. I’ve not tested this method of Cloudman Galaxy initialization, but I’m assuming it should work really well.
ASBMB policy blog just posted a concise summary of what impact sequestration could have on NIH and NSF funded research.
Today, the administration’s Office of Budget Management (OMB) released its plan, and it paints a pretty grim picture for biomedical research. The NIH and NSF would each sustain an 8.2% cut to their budgets which would amount to a reduction of roughly $2.5 billion and $460 million, respectively.
An 8.2% budget cut doesn’t mean that we are “trimming the fat”, or keeping expenses under control. I’m also not sure if it means we’ll be losing many jobs either. The scientific community is closely knit, and funding has been stagnant for a few years. We’ll keep doing some research, but not as much, and the size of incoming graduate student cohorts will continue to dwindle as training grants become smaller. I’m not sure whether this last part is overwhelmingly good or bad. Continue reading