Some short slide decks from a recent Bioinformatics Core workshop

Last week I helped teach at a workshop organized by the Bioinformatics Core facility of the UC Davis Genome Center. The workshop was on:

  • Using the Linux Command Line for Analysis of High Throughput Sequence Data

I like that the Bioinformatics Core makes all of their workshop documentation available for free, even if you didn't attend the workshop. So have a look at the docs if you want to learn about genome assembly, RNA-Seq, or learning the basics of the Unix command-line (these were just some of the topics covered).

Anyway, I tried making some fun slide decks to kick off some topics. They are included below.

 

This bioinformatics lesson is brought to you by the letter 'D'

'D' is for 'Default parameters', 'Danger', and 'Documentation

 

This bioinformatics lesson is brought to you by the letter 'T'

'T' is for 'Text editors', 'Time', and 'Tab-completion'

 

This bioinformatics lesson is brought to you by the letter 'W'

'W' is for 'Worfklows', 'What?', and 'Why?'

Genome Assembly: the art of trying to make one BIG thing from millions of very small things

Here are the slides from a talk I gave this week at UC Davis (also embedded below). This talk was for a group of graduate students (from different backgrounds). 

Note, because I tend to make very visual slides which don't always work well in isolation (you need to hear my sparkling narrative!), I have taken time to duplicate many slides and embed notes to indicate approximately what I would have said to explain the slide.

Identical Classifications In Science: Some advice for Jonathan Eisen

Jonathan Eisen — a colleague at the UC Davis Genome Center — has a quandary. He came up with a name for one of his projects but now needs to consider renaming it. The problem is that ICIS (Innovating Communication in Scholarship) sounds a bit like…well you all know what it sounds like. So Jon has appealed for suggestions on how to rename their project.

He should take comfort that he may not be the only one facing this dilemma. After all, the International Cooperative ITP Study Group (ICIS) has been an ongoing collaboration between hematologists since 1997. I wonder whether they are considering a name change? Maybe Jon could also ask the folk at the International Conference on Information Systems (ICIS) who have been meeting since 1980. Or they could talk to the people that came up with the Intelligent Coin Identification System (ICIS), or the The Intensive Care Infection Score (ICIS), or the Integrated Crate Interrogation System (ICIS), or the 20 year old International Crop Information System (ICIS), or the people who named this gene.

These are just some of the academic uses of ICIS that I could find from a couple of quick searches. I expect that there are more out there. This is a reflection on one of the most primal desires of all scientists…the need to come up with an acronym or initialism for their project. This urge is all too commonly associated with the additional need to make the name 'fun' (particularly a desire to name things after animals). Acronyms can also backfire for other reasons, such as when you don't fully appreciate how it might sound in other countries.

The shorter your acronym, the more likely that it has been used by other people before you (even within the same field). My suggestion would be to consider the shocking alternative of not using an acronym at all! After all, sometimes people can come up with new names that seem to catch on.

How does the popularity of the UC Davis Genome Center vary with geographic location?

If I perform a Google search for the two words genome center, I see that the UC Davis Genome Center (henceforth UCDGC) is the top hit. But this is to be expected because Google has been personalizing search results for some time now, so this result is obviously tailored to me (if you didn't know, I work at the UCDGC).

If you are signed in to Google when you perform a search, the results will be heavily influenced by your search history and by what Google knows about you and your interests. Even if you sign out of Google, the search engine giant can track some information via cookies. Even if you disable cookies or use a private browsing mode, Google is still altering your search results because it knows your location (even if only approximately).

This explains why I will almost always see UCDGC as the top result when I search for 'genome center'. To get around this, I could use a search engine that doesn't track my activity, or I could use a private browsing mode in combination with a little-known feature of Google, that of changing your search location. It's possible to perform a search as if I was located in any major city or state in America.

So this allows me to see how often the UCDGC appears in the #1 position as I move around the country. I first performed a search for 'genome center' as if I was located in each state (e.g. set location to be 'Alabama', 'Alaska', 'Arkansas' etc.):

Ranking of UC Davis Genome Center among Google search results when searching for 'genome center' in each state

When you search for 'genome center', the UCDGC is the top search result in every state! One caveat to this approach is that it may not be all that meaningful to set your location to be an entire state. So I repeated the approach but this time I set my location to be the most populous city in each state:

Ranking of UC Davis Genome Center among Google search results when searching for 'genome center' in the most populous city of each state (as indicated by position of marker within each state). 

This shows that UCDGC is the #1 search result for cities in 36/50 states. The places where UCDGC is not #1 are all cities that have a notable genome center of their own (or are located close to one). A few notes relating to this:

  1. The New York Genome Center dominates results not only in New York City (NY), but also in Newark (NJ), Bridgeport (CT), and Philadephia (PA)
  2. The #1 result in Baltimore (MD) is for the Institute of Genome Sciences at the University of Maryland
  3. St. Louis (MO) sees The Genome Institute at Washington University take the top spot
  4. In the north west, a search from Seattle gives the Seattle Structural Genomics Center for Infectious Disease as the most popular result. But if you head to Spokane (Washington's 2nd city), then the UCDGC becomes the #1 result again
  5. In Texas, the Department of Genomic Medicine at the Houston Methodist Research Institute, pushes UCDGC to 4th place. However, move to San Antonio or Dallas and the UCDGC regains first place
  6. Chicago (IL) has the Institute for Genomics and Systems Biology at #1
  7. In Minneapolis (MN) it is the University of Minnesota Genomics Center who is the top dog
  8. The home of the King (Memphis, TN) is also home to the W. Harry Feinstone Center for Genomic Research which takes the #1 position. Once again, if you move to this state's second city (Nashville), the UCDGC regains the top spot in the search results.
  9. Las Vegas, NV is home to the University of Nevada Las Vegas Genomics Core Facility. Moving to Nevada's second city (Henderson) puts UCDGC back on top.
  10. In Salt Lake City (UT) you can find the Utah Genome Depot at the University of Utah dominating the rankings.
  11. Finally, in Atlanta (GA), it is the Emory University Integrated Genomics Core which denies the UCDGC the #1 position

The UC Davis Genome Center is not only the top hit when you search for 'genome center' in various locations in the USA. If you use the Google location option to go truly global, you will see that we rank as the top search result for 'genome center' in London, Paris, Berlin, Moscow, Dehli, Seoul, Cairo, Buenos Aires, Bogota, Rio de Janeiro, Cape town, Kuala Lumpur, and Sydney!

While this could all be the result of UC Davis spending millions of dollars to adopt search engine optimization strategies to unduly influence our position in the search results, I prefer to believe that it reflects our reputation for world-class genomics research and training.

5 things to consider when publishing links to academic websites

Preamble

One of the reasons I've been somewhat quiet on this blog recently is because I've been involved with a big push to finish the new Genome Center website. This has been in development for a long time and provides a much needed update to the previous website that was really showing its age. Compare and contrast:

The old Genome Center website…what's with all that whitespace in the middle?

The new Genome Center website, less than 24 hours old at the time of writing.

This type of redesign is a once-in-a-decade event, and provides the opportunity not just to add new features (e.g. proper RSS news feed, twitter account, YouTube channel, respsonvive website design etc.), but also to clean up a lot of legacy material (e.g. webpages for people who left the Genome Center many years ago).

This cleanup prompted me to check Google Scholar to see if there are any published papers that include links to Genome Center websites. This includes links to the main site and also to all of the many subdomains that exist (for different labs, core facilities etc.) It's pretty easy to search Google Scholar for the core part of a URL, e.g. genomecenter.ucdavis.edu and I would encourage anyone else that is looking after an aging academic website to do so.

Here are some of the key things that I noticed:

  1. Most mentions of Genome Center URLs are to resources by Peggy Farnham's lab. Although Peggy left UC Davis several years ago (she is now here), her — very old, and out of date — lab page still exists (http://farnham.genomecenter.ucdavis.edu).
  2. Many people link to Craig Benham's work using http://genomecenter.ucdavis.edu/benham/. This redirects to Craig's own lab site (http://benham.genomecenter.ucdavis.edu), but the redirect doesn't quite work when people have linked to a specific tool (e.g. http://genomecenter.ucdavis.edu/benham/sidd). This redirects to http://benham.genomecenter.ucdavis.edu/sidd which then produces a 404 error (page not found).
  3. There are many papers that link to resources from Jonathan Eisen's group and these papers all point to various pages on a domain that is either down or no longer in existence (http://bobcat.genomecenter.ucdavis.edu).

There is an issue here of just how long is it valid to try to keep links active and working. In the case of Peggy Farnham, she no longer works at UC Davis, so is it okay if I redirected all of her web traffic to her new website? I plan to do this but will let Peggy know so that she can maybe arrange to copy some of the existing material over to her new site.

In the case of Craig's lab, maybe he should be adding his own redirect links for tools that now have new URLs. What would also help would be to have a dedicated 404 page which might point to the likely target page that people are looking for (a completely blank 'not found' page is rarely ever helpful).

In the case of Jonathan's lab, there is a big problem here in that all of the papers are tied to a very specific domain name (which itself has no obvious naming connection to his lab). You can always rename a new machine to be called 'bobcat', but maybe there are better things we should be doing to avoid these situations arising in the first place…

5 things to consider when publishing links to academic websites

  1. Don't do it! Use resources like Figshare, Github, or Dryad if at all possible. Of course this might not be possible if you are publishing some sort of online software tool.
  2. If you have to link to a lab webpage, consider spending $10 a year or so and buying your own domain name that you can take with you if you ever move anywhere else in future. I bought http://korflab.com for my boss, and I see that Peggy Farnham is now using http://farnhamlab.com.
  3. If you can't, or don't want to, buy your own domain name, try using a generic lab domain name and not a machine-specific domain name. E.g. our lab's website is on a machine called 'raiden' and can be accessed at http://raiden.genomecenter.ucdavis.edu. But we only ever use the domain name http://korflab.ucdavis.edu which allows us to use a different machine as the server without breaking any links.
  4. If you must link to a specific machine, try avoiding URLs that get too complex. E.g. http://supersciencelab.ucdavis.edu/Tools/Foo/v1/foo_v1.cgi. The more complex the URL, the more likely it will break in future. Instead, link to your top level domain (http://supersciencelab.ucdavis.edu) and provide clear links on that page on how to find things.
  5. Any time you publish a link to a URL, make sure you keep a record of this in a simple text file somewhere. This might really help if/when you decide to redesign your website 5 years from now and want to know whether you might be breaking any pre-existing links.

 

Designing a musical motif for the UC Davis Genome Center

Over the last month, I have spent much of my time helping to develop a new website for the UC Davis Genome Center (a site which will hopefully be launched very soon). In trying to bring the website into the modern era, I've been trying to set things up so that we can better promote any news that arises from the work of the talented faculty, staff, and students that we have.  

In particular, I'm keen to feature some video clips on the new site, and that made me think that we should have our own Genome Center 'ident' to use in any videos. Idents are a bit like stingers on radio stations, something that gives an audio signature that people might come to recognize (and maybe even like).

I have a smattering of music knowledge so I thought it might be fun to create something based on DNA. As there are four canonical DNA bases (A, C, G, and T), I thought that the musical motif should have four principle notes. I then decided to arrange the notes with musical intervals based on the intervals between the alphabet positions of A, C, G, and T. If you start this sequence on a C note, you end up with C, D, F# and G (one octave up). This progression feels like it needs to be resolved, and a basic G major chord seems to work.

So this is what I have come up with so far. This may end up being vetoed by the powers-that-be, but I'm still pretty happy with it:

Update: just to add that this piece was made entirely using GarageBand on my Mac. There are: three tracks that use Classic Electric Piano (I was using the onscreen keyboard which is why I ended up doing these as three separate tracks); one Tonewheel Organ track; one Upright Studio Bass track; one Classic Analog Pad track; and one String Ensemble track. The latter three tracks combine to form the final chord.

Top twitter talent: UC Davis genome scientists lead the way

The Next Gen Seq website has just published its 2013 list of the Top N Genome Scientists to Follow on Twitter. Over 10% of this International list of scientists are all staff or Faculty here at UC Davis, which says a lot about the quality of genomics talent here on campus:

It is also worth mentioning that there are so many other people at UC Davis who work in genomics and bioinformatics and who use twitter to effectively communicate their research and engage with the community. E.g.

  • @dr_bik - Holly Bik (Postdoc in Jon Eisen's lab)
  • @ryneches - Russel Neches  (Grad student in Jon Eisen's lab)
  • @theladybeck - Kristen Beck (Grad student in Ian Korf's lab)
  • @sudogenes - Gina Turco (Grad student in Siobhan Brady's lab...and winner of best twitter account name)

Great to see UC Davis recognized like this.

 

Update

Updated at 9:09 am to reflect that Next Gen Seq have now added Vince Buffalo to the list (he was apparently meant to be on the list anyway).

Some free code editors for Macs (that work in a UC Davis computer lab)

Every year I help teach a course[1] to grad students that hopefully leaves them with an understanding of how to use Unix and Perl to solve bioinformatics-related problems. We use a Mac-based computer lab because all Macs come with Unix and Perl installed. Many of our students are new to programming and many are new to Macs. Because of this, and because they need to use a code editor to write their Perl scripts, we have previously pointed them towards Fraise. Despite its age [2], this relatively lightweight editor has proved fine for the last few years that we have taught this course.

This year, however, Fraise proved problematic. The computer lab has now upgraded to OS X 10.8 which provides extra safeguards about what apps can be run. This Gatekeeper technology has been set up to only allow ‘signed’ apps[3]. The version of Fraise that we were using required administrator privileges for it to be opened (not possible in this computer lab).

My first thought was to direct students to download and install TextWrangler. This is an excellent, powerful, and well maintained code editor for Macs. Most importantly, it is free and also a signed app. However, it does try to install a helper app which caused a persistent dialog window to keep popping up during the installation. Clicking ‘cancel’ worked…but only after about 20 attempts[4]. I like TextWrangler as an app, but prefer the cleaner look of Fraise. So today I set out to find code editors for Macs that:

  • were free
  • could be run on the Macs in our computer lab (i.e. had to be signed apps)
  • were relatively simple to use and/or were easy on the eye

Here is what I came up with. These are all apps that seem to be under current development (updated at some point in 2013):

AppSize in MB Free? Notes

Komodo Edit301.1YesBig because it is part of a larger IDE tool which is not free[5]

Sublime Text 227.3sort of[6]Gaining in popularity (a version 3 beta is also available)

TextMate 230.3YesWhile this is technically an ‘alpha’[7] release, it seems very stable.

TextWrangler19.2YesVery robust and venerable app. Free since 2005

Tincta 25.6YesSmall app, similar to Fraise in appearance

 

If I had to suggest one, it would probably be Sublime Text 2 (though I will encourage students to buy this if they like it). TextMate 2 is a good second choice, particularly because it is also a very clean looking app. Of course, at some point we need to tell students about the joys of real text editors such as vi, vim, and emacs…but of course this might lead to hostilities![8]

  1. This course material is available for free and became the basis for our much more expansive book on the same topic  ↩

  2. Fraise is itself a fork of Smultron which stopped development in 2009 but which reappeared as a paid app in the Mac App Store in 2011.  ↩

  3. Those apps that are approved by Apple, even if they are not in the Mac App Store.  ↩

  4. Seriously, it takes a lot of clicks to make this dialog box go away. It then produces more pop-up dialogs asking whether you want to register, or install command-line tools.  ↩

  5. Currently $332 for a single license  ↩

  6. This is a paid app, but can be used in trial mode indefinitely with occasional reminders.  ↩

  7. TextMate 2 has been in alpha status since 2009  ↩

  8. Editor wars should be avoided if possible  ↩

How well do UC Davis Graduate Groups communicate their work to the wider world?

PhD students in our lab are mostly split between a couple of UC Davis's many graduate groups. A conversation with some of the students today about 'outreach' and 'social media' led me to wonder how well these graduate groups are communicating their presence to the outside world. The simplest ways of doing this would be:

  • maintain a current website for your graduate group (i.e. with news items)
  • use Facebook (ideally with an open group)
  • establish a blog
  • use twitter

I looked at 11 different graduate groups to see how well they ticked the above boxes. I might be missing some blogs, Facebook groups, and twitter accounts, but if I can't find the relevant details from a Google/Facebook/Twitter search, then I'm assuming that others won't discover them either. This is what I found:

Headline links take you to the home page for the respective graduate group.

Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB)

  • No news page but has an actively maintained blog (easily linked to from above site)
  • Facebook group (open)
  • Active twitter account

Biomedical Engineering (BME)

Biostatistics

  • No news page, though there is a short 'announcements' box on main page
  • No Facebook group
  • No twitter account

Ecology

Epidemiology

  • No news page
  • Facebook group (closed)
  • No twitter account

Integrative Genetics and Genomics (IGG, formerly GGG)

  • Has a news page, but only one item from 2013, remaining items from 2009 and 2008!
  • Facebook group (closed, and have to search for GGG or IGG to find it)
  • No twitter account

Immunology

  • No news page
  • No Facebook group
  • No twitter account

Microbiology

  • No news page
  • Facebook group (closed)
  • No twitter account
  • Has separate website
  • Other: website told me I had to enable Javascript to view their home page even though I have javascript enabled

Nutritional biology

  • No news page
  • No Facebook group
  • No twitter account

Plant Biology

  • No news page
  • No Facebook group
  • No twitter account

Population Biology

  • No news page
  • No Facebook group
  • No twitter account

Please let me know of any updates or additions that I can make to this list

So overall it is pretty poor. BMCDB outshines the others, though BME and Ecology also have a good presence on the web. In many ways, I think it looks worse to do these things badly than to not to them at all. Closed Facebook groups don't send out an inviting message, and having a 'news' page for your graduate group with items from 5 years ago, also sends out the wrong signals.

It takes time and effort to maintain a social media presence, but it doesn't take much effort to at least maintain a news page or simple twitter account (even posting just 1–2 times a week is better than nothing).

Furthermore, the ability to show that you can communicate your work to the wider world is of increasing relevance when applying for grants. It can also raise your profile with your peers and be a useful addition on a resume that helps you stand out from other applicants. Finally, starting a blog or twitter account also helps you hone your writing skills (the latter is great for making you think about how to condense complex thoughts into 'bite size' chunks).

I hope that some of UC Davis's graduate groups make more of an effort in this area (and of course the same can be said for many of UC Davis's departmental and lab websites).

 

Updated 26th September: Added details of some graduate groups that do have blogs and/or websites but which, unhelpfully, are not linked to from their official graduate group webpage.