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Showing posts with label RSS. Show all posts
Showing posts with label RSS. Show all posts

How to Stay Current in Bioinformatics/Genomics

A few folks have asked me how I get my news and stay on top of what's going on in my field, so I thought I'd share my strategy. With so many sources of information begging for your attention, the difficulty is not necessarily finding what's interesting, but filtering out what isn't. What you don't read is just as important as what you do, so when it comes to things like RSS, Twitter, and especially e-mail, it's essential to filter out sources where the content consistently fails to be relevant or capture your interest. I run a bioinformatics core, so I'm more broadly interested in applied methodology and study design rather than any particular phenotype, model system, disease, or method. With that in mind, here's how I stay current with things that are relevant to me. Please leave comments with what you're reading and what you find useful that I omitted here.

RSS

I get the majority of my news from RSS feeds from blogs and journals in my field. I spend about 15 minutes per day going through headlines from the following sources:

Journals. Most journals have separate RSS feeds for their current table of contents as well as their advance online ahead-of-print articles.
Blogs. Some of these blogs are very relevant to what I do on the job. Others are more personal interest.
Forums.

Mailing lists


I prefer to keep work and personal email separate, but I have all my mailing list email sent to my Gmail because Gmail's search is better than any alternative. I have a filter set up to automatically filter and tag mailing list digests under a "Work" label so I can get to them (or filter them from my inbox) easily.

  • Bioconductor (daily digest)
  • Galaxy mailing lists. I subscribe to the -announce, -user, and -dev mailing lists, but I have a Gmail filter set up to automatically skip the inbox and mark read messages from the -user and -dev lists. I don't care to look at these every day, but again, it's handy to be able to use Gmail's search functionality to look through old mailing list responses.

Email Alerts & Subscriptions

Again, email can get out of hand sometimes, so I prefer to only have things that I really don't want to miss sent to my email. The rest I use RSS.
  • SeqAnswers subscriptions. When I ask a question or find a question that's relevant to something I'm working on, I subscribe to that thread for email alerts whenever a new response is posted. 
  • Google Scholar alerts. I have alerts set up to send me emails based on certain topics (e.g. [ rna-seq | transcriptome sequencing | RNA-sequencing ] or [ intitle:"chip-seq" ]), or when certain people publish (e.g. ["ritchie md" & vanderbilt]). I also use this to alert me when certain consortia publish (e.g. ["Population Architecture using Genomics and Epidemiology"]).
  • PubMed Saved Searches using MyNCBI, because Google Scholar doesn't catch everything. I have alerts set up for RNA-seq, ChIP-Seq, bioinformatics methods, etc.
  • GenomeWeb subscriptions. Most of these are once per week, except Daily Scan. I subscribe to Daily Scan, Genome Technology, BioInform, Clinical Sequencing News, In Sequence, and Pharmacogenomics Reporter. BioInform has a "Bioinformatics Papers of Note", and In Sequence has a "Sequencing papers of note" column in every issue. These are good for catching things I might have missed with the Scholar and Pubmed alerts.

Twitter

99.9% of Twitter users have way too much time on their hands, but when used effectively, Twitter can be incredibly powerful for both consuming and contributing to the dialogue in your field. Twitter can be an excellent real-time source of new publications, fresh developments, and current opinion, but it can also quickly become a time sink. I can tolerate an occasional Friday afternoon humorous digression, but as soon as off-topic tweets become regular it's time to unfollow. The same is true with groups/companies - some deliver interesting and broadly applicable content (e.g. 23andMe), while others are purely a failed attempt at marketing while not offering any substantive value to their followers. A good place to start is by (shameless plug) following me or the people I follow (note: this isn't an endorsement of anyone on this list, and there are a few off-topic people I follow for my non-work interests). I can't possibly list everyone, but a few folks who tweet consistently on-topic and interesting content are: Daniel MacArthur, Jason Moore, Dan Vorhaus, 23andMe, OpenHelix, Larry Parnell, Francis Ouellette, Leonid Kruglyak, Sean Davis, Joe Pickrell, The Galaxy Project, J. Chris Pires, Nick Loman, and Andrew Severin. Also, a hashtag in twitter (prefixed by the #), is used to mark keywords or topics in Twitter. I occasionally browse through the #bioinformatics and #Rstats hashtag.
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Pubmed Searches as an RSS feed

As Stephen nicely posted earlier, RSS feeds are a very powerful way to keep up with the literature -- they "push" the information to you. In addition to subscribing to individual journals, you can subscribe to a PubMed search! This will let you keep up with ALL PubMed indexed journals.

To subscribe to a PubMed search, first go to www.pubmed.org and enter your search terms. Once you retrieve a search listing, you'll see a bar that says

Display Summary Show 20 Sort By Send to

The SEND TO drop down box will allow you to select an RSS Feed. Once you select this, you'll be taken to a page with a button that says "Create Feed". When you click this, you'll get a new page with a little orange XML button. Click it and your browser will give you the option to subscribe to the feed. Once you subscribe, there are lots of ways to read RSS Feeds, which we'll probably get to in another post.

Enjoy!
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Start using RSS in 5 minutes

RSS rocks. In addition to consolidating all the news you read on a single page, it's also handy for keeping up with the latest publications in your favorite journals without ever going to PubMed. If you're not using RSS, give it a shot and you'll never look back.

RSS stands for Really Simple Syndication. You might also hear it called "syndication", "news aggregation", "news feeds", or simply a "feed." Nowadays, nearly every blog, news, or other website that continually updates content uses RSS and allows users to subscribe to those feeds, and that includes most scientific journals. CNN, Nature Genetics, PNAS, Getting Genetics Done, ESPN, and even Barack Obama's blog all broadcast RSS. An RSS reader will aggregate updates or headlines from your favorite websites as they are posted into a single page, and usually lets you read the first paragraph or so of the article. You can then click to link out to the full article and continue reading if you're interested. It's a great way to aggregate all the news or blog content you read on a daily basis into a single web page for quick viewing.

To start using RSS, you'll need a reader. A great one to start with is google reader. They have a one-minute long video to show you the basic features. It's web-based so you don't have to install anything. All you need is a Gmail account, which most people already have nowadays.

Now let's subscribe to a few posts. Go to the NY Times' Science page. If you're using firefox, you should see the shiny orange RSS symbol in the address bar. Internet Explorer and Chrome have similar functionality built-in. Click it, then click add to Google Reader. Let's add a subscription to Nature Genetics. Click on their "Web Feeds" link near the right hand side of the front page. If websites don't have a page dedicated to the feeds they offer, many times your browser will realize that the content is syndicated with RSS, and you can subscribe using your browser. Now go back and check out your google reader page. It's easier to skim through headlines if you click the "Show: List" view rather than the expanded view. Click "Mark all as read" when you're done scanning through headlines. Any new stories published on either of these websites will show up here as a new item.
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