Oldest Reading hard copy tables of content. Pleasent, but impractical.
Older Checking out the updates for Index Medicus. Totally reasonable. In 1988.
Old Getting eTOCs emailed to you. Welcome to the year 2000.
Middle-aged Subscribing to RSS feeds for journals. Okay, but still needs filtering.
Present Automated, keyword-based filtering of RSS feeds. Better.

RSS feeds

E.g., here are the ones for Nature journals (including the AOPs) (link)
And for Science (link).
It doesn’t take much time to find feeds for the top 20 journals in your field. Feed links shouldn’t change frequently, but they can change.

Filtering RSS feeds

This is an early (2005) work in the field of filtering RSS feeds from journals: BaRF (Bioinformatics aggregated RSS feeds) is a tool for keeping up with bioinformatics articles across multiple journals’ RSS feeds.

Presently, there are a bunch of different ways to filter RSS feeds. Fascinatingly, they’re all inadequate. So, although this is a good approach, I’m not sure it’s worth the time to set up and maintain just yet.

At any rate, if you want to take a stab at it, here are some of the services to check out. Feed Sifter, Scraper, Superfeedr, Feed Rinse. To be honest, none of these worked completely for me. I’ve tried others as well, including the powerful Yahoo Pipes (too buggy). If you have a system worked out that you’d like to share, please let us know.

Getting every last drop

It’s also possible to set up PubMed search result updates. But there can be weeks between when an article is put online and when PubMed picks it up, so this isn’t ideal. However, it covers all of the journals that PubMed indexes, so it can bring papers to your attention that might have otherwise fallen through the cracks of your RSS feeds.

Services like Hubmed and Mendeley are trying to serve this need from a different angle, but at present don’t offer the immediacy of an RSS feed of AOPs.

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1 comments

Online catalogs

For small things, I pick vendors based on a few key criteria, the biggest one is how easy it is to find what I want on their web site. (The other factors are delivery time and if they’ll take a PO without needing any other information from me.)

McMaster-Carr has the best web site I’ve ever used (pictured above). It’s fast and intuitive to find what I’m looking for, and the information I need in order to select the right product is right there on the product pages (I don’t have to click through to a PDF or run a Google search to remind myself which type of aluminum is the lightest). It’s way ahead of the competition. Aesthetically, their all B&W line drawing look is pleasing, but it would be nice if I could get a color photo at some point in the search. Thier search interface works so well that sometimes I just use it to find a manufacturer item code, which I then use to find something on a different company’s web site.

Digikey recently released their Dynamic Catalog and it’s wildly underwhelming. As far as I can tell, it’s simply a reformatting of a portion of their offerings. Their basic search system (pictured below) is showing its age, but it’s decent.

Mouser’s web site is functionally similar (below).

Sparkfun’s web site is well done. They have a relatively limited catalog, so it’s easier for them to keep things nice without needing a complex search interface. What’s really nice is the discussion thread on each item’s page.

Thorlabs’ web site deserves high praise as well.

Related post: Catalogs as Textbooks (popular)

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Lab accidents do happen. Fortunately they’re rare because of safety measures. Unfortunately, this also makes people lazy about following safety guidelines.

Earlier, Labrigger covered the danger of retinal burns with lasers.

Cautionary tales are perhaps effective against the safety negligence that sets in when accidents are rare. Here are some more quick examples of bad lab accidents that may have been avoided with closer adherance to safety standards:

- In 2010, a student lost three fingers, sustained burns to his hands and face, and injury to his left eye after a lab explosion. There were several safety issues, including exceeding safe quantities.

- In 2008, Sheri Sangji, a 23-year-old lab tech, was burned in a chemistry lab accident at UCLA, and died 18 days later. CalOSHA determined that safety negligence was an issue. There have been fines and felony charges.

Lethal accidents happen in biology labs as well.
- In 2009, Malcom Casadaban, a professor at U Chicago, died from an infection by an attenuated strain of a BSL-2 bacteria, Yersinia pestis (yeah, that one). He was known to not use gloves when handling cultures and dermal exposure may have been the preventable route of entry.

Please be safe.

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The Labrigger editorial team was a little disappointed in the consistently excellent xkcd when the recently posted list of approximations included:
Number of seconds in a year = 75^4 (accurate to 1 part in 400)
and
Number of seconds in a year = 525600 x 60 (accurate to 1 part in 1400)

In our physics classes, we always used:
Number of seconds in a year = Pi x 10^7 (accurate to 1 part in 200)
It’s still very accurate. And most importantly, the factor of Pi makes for some fascinating cancellations in calculations.

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You probably already know that many grants have, in addition to the direct component that goes to the lab, an indirect component that goes to the institution.

US institutions negotiate with the NIH to set a percentage for all awards. For example, here are Harvard’s (relatively high) indirect rates. These indirect funds are used by departments and institutions to keep the lights on, pay admin staff, cover startups, and other important things.

A recent Nature article by Paula Stephan offers this insight into one aspect of how indirect rates are set:
“A US government accounting rule called A21 means that the more debt universities have from construction, the more they can add to grants for overhead costs. If a university borrows $100 million to build a new facility and pays 4% interest, it can increase its indirect rate by including the $4-million interest payment in the calculation. ”

The article concludes with, “Perhaps it is time for deans in the biomedical sciences to rent some of that excess space to their colleagues in chemistry and physics.”

Has biomedical research grown too big? Does it need to contract? Or is it only PhD programs that need to contract? On that topic, the article also suggests making graduate students more expensive to academic labs, and staffing labs with more professional scientists.

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The Society for Neuroscience (SfN) have compiled and are curating a large collection of online resources for neuroscience teaching. It’s called ERIN (Educational Resources in Neuroscience).

Some examples:
A Nernst-Goldman equation simulator. (link)

An animation discussing the structure and function of the cochlea. (link)

An interactive tutorial on nuclear receptor signalling. (link)

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Nature has a special issue on the future of PhDs. It’s no secret that unlike the US MD program, PhD programs are not regulated and produce way more PhDs than there are jobs for PhDs.

The articles in the issue offer some suggestions. Many seem straightforward and pragmatic, such as studying the demand for PhDs in the workforce, and then changing PhD program sizes and training to match that demand, rather than the needs of academic laboratories.

I’d like to see this idea get some sort of momentum. We need a Flexner Report for PhDs. It won’t be the same, of course. For many reasons including the fact that medicine is arguably a more stereotyped practice than the varied work that PhDs do. However, the MD system is infinitely better regulated than the PhD system and there’s certainly a thing or two to be learned from it.

Perhaps these issues will be addressed on a field-by-field basis. For example, the prospects for economics PhDs are actually pretty good. They have a decent system in place. Why doesn’t this happen in other disciplines? Here’s one opinion.

The articles in the special issue of Nature offer some interesting statistics, such as the growth of PhDs granted across different countries.

BTW, here’s the annual population growth for some of those countries, for reference. They’re all right around 0-1% for the time period covered above. (source)

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Light field imaging is a very interesting approach to imaging. The idea is to use an array of microlenses in order to capture light coming from many different angles. By storing this data, it is possible to bring different focal planes into focus in post-processing offline. It has been implemented for wide-field microscopy.

The Stanford Computer Graphics Laboratory has released some Mac OSX software for trying this yourself. Their website includes information on how to build the imaging rig out of Thorlabs parts. It’s open source (GNU).

It’s not new technology. In it’s current form it dates back to at least the 1990′s. However, just recently (started shipping in February) it has been commercialized into a consumer camera by Lytro, a company started by an alumnus of the Stanford group.

Below is an example of output from the Lytro camera. Single click on a part of the image to bring it into sharp focus.

Labrigger is currently waiting for their Lytro camera to arrive.

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The Movshon-Seung debate on what priority connectomics should be is now on YouTube.

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