Posts tagged with references
Here’s a follow up on the previous post about alternatives to Google Reader (which is being shut down).
Patrick Mineault commented that Feedly is looking good. I agree. Basic functionality is smooth and somewhat intuitive; layout and design are excellent.
Google Reader is going to be shut down on July 1.
If you use Reader, here’s what to do:
Step 1: Export all of your subscriptions from Google Reader
(takes less than 1 minute)
Try these directions. It’s easy.
Step 2: Start using an alternative, and import your old Google Reader stuff.
(can take as little as 2 minutes, once you decide on one)
I’m trying Bibliogo right now, and I like it so far. It’s geared towards academics, so it’s a good fit for the Labrigger audience. It opens webpages within the window in a nice way, making it fairly quick to flip back and forth between RSS entries and the actual webpages. Even Google Reader never did that very well.
But there are other alternatives.
WordPress has a Google Reader-like feature.
SmashingReader looks nice.
If you have your own server, you might like Fever or PrivateOSS.
Wolfgang Becker just gave a nice talk at the Berkeley Advanced Imaging Methods meeting.
I should add the Becker-Hinkl literature to the list of online references.
Previously
Catalogs as textbooks
Troubleshooting fluorescence microscopy
There are a lot of online, open course materials, e.g. MIT’s OpenCourseWare and Open.Michigan. OEDB.org’s Open Courses section is a bit of an aggregator and a good place to start any searches for online courses. Also, Open Textbooks specifically link to online, free, open textbooks.
(source for image above)
Hat tip to Daniel Strauss.
PubPeer, a site for anonymous (or non-anonymous), post-publication peer review is taking off nicely. Traffic is increasing to the site and there are a lot of interesting comments, including both detailed commentary and brief observations. Some discussions are getting quite involved (over 15 comments).
Since the last time Labrigger mentioned PubPeer, they’ve added some nice features.
1: Recent comments. (pictured above) shows the most recent activity on the site.
2: Alerts. Users can choose to receive email alerts whenever someone comments on their favorite
papers.
3: Simplified author signup. Get to commenting easier.
There will probably always be a need for metrics like impact factor so that non-experts can estimate the significance of a scientist’s publications. These metrics are problematic, as we all know.
Interestingly, the relationship between an article’s citation rate and its journal’s impact factor is weakening. The saturation of the market by many specialty journals, along with their widespread online accessibility, has resulted in a lot of top papers going to smaller, low impact factor journals. This preprint has the details:
The weakening relationship between the Impact Factor and papers’ citations in the digital age
George A. Lozano, Vincent Lariviere, Yves Gingras
Will this trend continue?
(source, arXiv)
Figshare is an online database for storing figures, data, and papers. It’s been around for a while, but recently its really been taking off.
–You can post images, or entire paper PDFs. Also datasets.
–It’s citable. Useful for negative data?
–It’s free.
–If you want to keep it private, the limit is 1 GB. If you leave it public, there is no storage limit.
Post publication peer review has yet to really take off, but Labrigger hopes it does. One of the newest sites is PubPeer.
PubPeer does it right, allowing for anonymity. This is important in order to obtain candid opinions from the scientific community. The bland and boring reviews at F1000 show what comes out when anonymity is not allowed.
An addition benefit is an increased quantity of participation: compare the content on Wikipedia and Scholarpedia. The latter has non-anonymous authorship, and although the articles are high quality, the quantity is very poor compared to Wikipedia. Anonymity lowers the threshold for making casual additions to online resources.
PubPeer is not a free-for-all, however, it is trying to keep the comments constructive by only allowing authors of papers to create accounts and comment.
A similar effort, The Third Reviewer, seems to have been abandoned. I get the impression that the PubPeer platform is a bit better automated than The Third Reviewer, so perhaps it has more staying power.
One concern is that anonymity will mean the comments will be dominated by cranks and disgruntled colleagues, and might even devolve to the level of YouTube comments. However, as evidence to the contrary, the comments on the short-lived Third Reviewer site were all fairly constructive and generally positive, even when pointing out technical flaws or other issues (examples 1, 2, and 3).
“Okay. I think I’ve got a lead on the noise we’ve been troubleshooting. The noise is coming from a broadcast RF source between 2200 and 2500 MHz. Let’s check with the FCC and see what is allocated to that spectrum to get an idea of where this interference could be coming from.”
“Right.”
Here’s the full FCC allocation map– or at least a snapshot from 2011.
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.
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.
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.
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.