That's no moon…but it is one of my favorite places to visit in Davis

Some may know it as the UC Davis Social Sciences and Humanities Building, but for me it will always be the Death Star. It's an amazing building…well technically it is a collection of many interconncted buildings, all packed with awkward, imposing angles. It is very easy to get lost in the innards and courtyards of this building, and this (intentional) design feature is part of the charm.

No two corners (or windows) appear to be the same and there are many steps that lead you to dark nooks and crannies. Perfect spots for plotting the destruction of those Rebel scum.

If you have never visited the Death Star, then you should give yourself to the Dark Side (at least once!). Here are some black and white photos that depict the Death Star in all of its raw and powerful beauty.

Click on the pictures to enlarge…

Thoughts on the unpredictability of which social media posts will be popular

I tweet a lot and I write a lot on my blogs, especially on my ACGT blog. Sometimes I write things where I think: This…this is the one that will go viral. And of course it never happens that way. The more I try to engineer a meme, the less likely the chance of success seems to be. This is why my concept of a #MexicanTweetOff never went anywhere, and that no-one seemed to get the joke in my recent #IamSpartacash tweet:

But then there are those tweets and blog posts which I think won't be of that much interest to anyone, but turn out to be the most popular things I've ever written. This week has been surprising in that two of my social media posts have taken on a life of their own.

Everyone loves a good gnome story

First, I spotted the opportunity to have a bit of fun with Genomics England. Last Thursday was a big news day for them with the project being featured in Nature. So after seeing the piece in Nature early on Thursday morning, I came up with this:

This tweet went on to have over 40 retweets and Genomics England ended up featuring me in a storify article on Friday about their news of the previous day. To date, that tweet has reached an audience of over 67,000 people on twitter!

Microsoft as a tool for bioinformatics

Then on Friday I was trying to find an image to use in a talk. I wanted to make a point about Excel often being an inappropriate tool for the management/querying of biological data, and just wanted a picture of Excel containing some sort of biological data. I was quite surprised by the image that I eventually found, and immediately shared it in a quick blog post:

Admittedly. the 'NFSW' part of the blog post title was a tactic designed to deliberately provoke curiosity. I tweeted about the blog post on Friday afternoon, a time which normally doesn't provoke a lot of interest (many of my European followers will have gone to bed by this point).

But it seems that this post hit a nerve and it has subsequently taken on a life of its own. Currently, there has been 64 retweets and 44 favorites, and now it is being spread on Facebook. By the end of Friday, it had become the most read item on my blog for the entire week (this never happens for posts I publish on Friday afternoons). I assumed that traffic would die down on Saturday but that didn't happen. By the end of Saturday, the post was my most read article of anything I have posted in the last 4 months.

At this point I assumed that things would surely quiet down on Sunday, but that didn't happen either. Traffic to my blog doubled compared to Saturday, and the post has now become the most viewed article of anything I have written in 2015, with almost 3x the page views compared to the next most-read article.

I guess the message here is that I should stop trying to predict the popularity of my social media posts!

Writing a new book

Just a quick note to say that I am currently writing a new book with the help of Michelle Gill and Ian Korf. This will be a follow up our Unix and Perl to the Rescue! book. The name?

Unix and Python to the Rescue!

Snazzy eh? You can find out more details about why we are doing this on the newly revamped Rescued by code! website (it didn't make sense to keep on using the unixandperl.com website anymore).

A flag for Davis, California

Yesterday was flag day in the United States. So it seems a fitting time to launch my idea for a flag for the city of Davis, California. Davis currently has a logo, which incorporates a Penny Farthing bicycle, but this is not a good choice for a flag as it breaks many rules of good flag design.

Here is my proposed design (you can also download a larger version without the border):

The video below explains what this design symbolizes. I shall contact the Davis City Council with my idea, but I would love it if they organized a proper flag designing competition, open to all residents of Davis.

Flags can be rallying symbols that a city can unite behind. Flags can also give people a sense of pride about where they live. So let's have a flag for Davis, California!

Video: iterating towards the final design of my 'These go to five' banner logo

I recently launched a new blog, These go to five, which is attempting to (very slowly) chronicle all of the five-star songs that make up my iTunes music library. These songs represent only about 1% of my ~13,000 song music collection, so I thought I would use the blog to explain why they are so special to me.

Once I had settled on the name — a bit of an oblique reference to these go to eleven — I then started work on my design for a banner logo. The following video shows how I iterated over several designs before arriving at the final version. The backing music is an instrumental song that I wrote as part of the RPM music challenge.

Which coalitions would have the greatest support from the electorate?

Time for some amateur psephology regarding the imminent UK general election. British voters have probably seen many, many graphs like this one which shows the projected share of the vote:

Data from electionforecast.co.uk

However, these type of graphs don't always reflect the picture among the entire electorate. That's because a sizable chunk of eligible voters do not vote. In the previous 2010 election, voter turnout was 65.1% and this is pretty close to the average from the last four elections (average turnout 64.1%). So let's assume that turnout on Thursday will be about the same, and I'll arbitrarily set it at 65%. This means that the 34.5% of people who are projected to vote Conservative are really drawn from the 65% of people who might actually vote. I.e. the percentage of the electorate who might vote Conservative is only 22.4%. So the most popular party — in terms of share of the vote — may only have the backing of fewer than 1-in-4 possible voters. Let's see how things look if we plot the support for each party based on the percentage of the electorate who might vote for them:

Of course, it's possible that the third or so of people who don't vote may all have strong leanings towards the Conservatives, or towards Labour, or it may be that the 35% contains a representative mix of supporters of all of the parties. I'm not sure if anyone has any good insight into political allegiances of this group of non-voters.

There is already a lot of speculation as to which coalition might end up coming together to form a workable government (there are a lot of permutations). So I'm curious about how well possible coalitions might reflect support from the electorate as a whole vs the combined number of seats they would amass as a voting block. To gain an absolute majority, any coalition would ideally need 325 of the 650 seats.

The following graph plots the number of seats that various Conservative and Labour coalitions might achieve vs the possible percentage of the electorate that might back such a coalition. I've also included separate data points for Conservative and Labour as potential minority governments (circles and squares indicate Conservative/Labour coalitions respectively):

So what does all of this mean? First let's look at the situation for the Conservatives:

  1. Another Conservative/Liberal Democrats coalition would have 307 combined seats, but would only have the backing of 30% of the electorate.
  2. Combining with the UK Independence Party (UKIP) might only give the Conservatives 1 more seat, but it adds a sizable chunk of electoral support (rising from 22.4% to 29.6%)
  3. If the Conservative could combine with the Lib Dems, UKIP, and the Democratic Unionists Party — a party from Northern Island who have often allied with the Conservatives in the past — then they would still only have 316 seats, and this would reflect potential backing of 37.6% of the electorate.
  4. It's hard to imagine any other party supporting the Conservatives, except for maybe on a vote-by-vote basis.

And for Labour:

  1. Support from the Scottish National Party (SNP) would add a huge number of seats to a potential coalition (which has already been ruled out), but would hardly change the national backing from the electorate. The SNP only run candidates in Scotland and despite potentially winning almost every Scottish seat, this may only reflect 2.5% of the electorate voting for them.
  2. In contrast, a Labour/Lib Dems coalition would gain fewer seats than a Labour/SNP deal (293 vs 318) but would end up reflecting much more support from the electorate.
  3. Labour have more potential coalition partners than the Conservatives, and could possibly form some sort of union with the SNP — yes, I know that I've already said that this has been ruled out but you know…politics — as well as the Lib Dems, the Greens, Plaid Cymru, and the SDLP (the Social Democratic Labour Party of Northern Ireland). If they all joined forces, they could amass 352 seats with backing from 34.7% of the electorate.

Conclusions

So in the unlikely scenario of grand Conservative or Labour coalitions, you still end up with a situation where less than 40% of the electorate would have voted for them. Only if Labour can unite with the SNP, will they have a chance of an absolute majority (>325 seats). The best they can do otherwise might be about 300 seats or so.

I find it interesting that the slice of the electorate who probably won't vote is larger than any single party, and larger than all of the potential coalitions listed above bar one (the grand Conservative coalition).

Whatever happens on Thursday — and over the following days and weeks — it will probably be true that any resulting coalition is going to be unpopular with most of the electorate.

Bad restaurant marketing in Davis: a sign of the times?

There is a relatively new Japanese restaurant in Davis. Like all restaurants, and most places of business, it has signage that displays the name of the restaurant. Here is how that sign looks when looking at it directly from about 20 feet away:

If you were driving past this establishment, you'd be another 20 feet or so away from the sign. I suspect that many of you might not be able to clearly read the first word. Here's a close up:

The shadows that you can see hint at the problem that I'm about to raise. This signage is 3-dimensional, with the letters being raised several inches from the wall. So what happens when you have such a sign and you try looking at it from anything other than directly head on?

Doesn't seem great from a marketing perspective if the name of your business can only be read when looking at your sign from one particular angle! It's a little better at night as the white backing to the letters is illuminated. Here is a close up that more clearly shows the 3-dimensional nature of the sign:

Did no-one check this at any point and ask the simple question "Wait, can you actually read those words?"

Sketches of Science: a must-see exhibition in Davis

This weekend we managed to catch the Sketches of Science exhibition at the Mondavi Center (also see the official website). I thoroughly recommend that people catch this free exhibition before it finishes on 28th January.

Photographer Volker Steger has met with many Nobel prize winners and asked them to make a poster (using crayons) that represents their nobel-prize-winning science. He then photographs them with their poster and some of the posters are also accompanied by audio interviews.

There is a lot of humor, beauty, and fun that emerges from this experience. Some scientists go for a simple representation of their work, others pack a lot into the poster (including a poem in one instance). Well worth seeing if you get a chance. I believe that this is the only place in the USA where this exhibit is being shown at the moment.

Martie Chalfie, one of many folks to win the nobel prize for their work on Caenorhabditis elegans

Bob Horvitz, another C. elegans researcher to feature in the exhibition

Decade

This Saturday marked by 10th year at UC Davis (also my 10th year of living in the USA). This is kind of incredible since the plan was only ever to stay for a year or two! Since arriving here in 2005, I have become a husband, a father, and settled down to a wonderful family life.

However, all good things come to an end and so we are planning to move back across the pond. We don't yet know where we will go (probably the UK, but possibly Western Europe), we don't know yet know what we we will do (probably something related to science), and we don't yet know when we will go (probably early 2016).

The USA, and Davis in particuar, has been very good to us both professionally and personally. Our careers have flourished, but more importantly we have made some wonderful friends who we expect to keep in close contact with wherever we end up.

I thought that this would be a fitting time to relaunch my website and blog as I plan to write more regarding what will be the next big chapter in our lives. The idea of not knowing where you will be in a year's time, or what you will be doing, is exciting and scary in equal measure.

I'm looking forward to what the future brings us.

No more science…at least not on this blog

I've decided that as I'm increasingly using this blog to write about science-related topics (bioinformatics in particular), that they should have a new home. Therefore, all of my existing genomics and bioinformatics blog posts have been copied to my new ACGT blog:

http://acgt.me

I have also removed these posts from this site so that (ultimately) they will only show up in one place in search engine results. Going forward, I will use the ACGT blog to write about anything that is predominantly science related. In contrast, this blog will now be used almost exclusively for stuff that is not primarily related to my research work.

 

Updated 2015-11-12  to reflect that I have now removed the posts that were duplicated between this blog and ACGT.

A stunning hyperlapse video of life on the UC Davis campus

A few days ago, UC Davis student Joe Na (@joenagraphy on twitter) released this hyperlapse video of scenes from around the UC Davis campus, and I've found myself captivated by it. 

UC Davis from Joseph Na on Vimeo.

One reason why I've been watching this video over and over again is because Joe has shot some superb scenes with amazing lighting, and it is just beautiful to watch. However, that's not the only reason why I'm so drawn to this video.

After nine years of working at UC Davis I realized just how connected I feel to many of the places that are included in this video. For most of the last two years I have abandoned cycling in favor of walking everywhere on campus. I'm based on the 'far side' of campus near Aggie Stadium, but frequent meetings, teaching requirements, and the need to get a bus home, all mean that I'm regularly walking all over campus.

When I first saw this video, I instantly recognized every location because in an average week, I walk past (or through) most of them! So here is my shot-by-shot breakdown of the video (with links to DavisWiki as appropriate): 

  1. 0:00–0:05 MU bus terminal
  2. 0:06–0:09 The western edge of the Quad, facing south
  3. 0:10–0:16 On the Quad, facing the MU
  4. 0:17–0:25 On top of the West Entry Parking Structure on Hutchinson Drive, looking southwest to the GBSF and the Health Sciences District
  5. 0:26–0:30 In the Arboretum by Lake Spafford, looking west
  6. 031–0:34 Looking west across Lake Spafford
  7. 0:35–0:38 Looking at 3rd & U Cafe from 3rd & University
  8. 0:39–0:42 Looking at Wellman Hall from the east side
  9. 0:43–0:47 Entrance of Warren & Leta Giedt Hall, with Kemper Hall in background
  10. 0:48–0:57 Two scenes inside the CoHo
  11. 0:58–1:02 Moving to outside the CoHo, overlooking the Quad
  12. 1:03–1:09 Back to the MU bus terminal, looking north
  13. 1:10–1:15 Outside the Mondavi Center
  14. 1:16–1:19 Central area of Olson Hall looking down to the basement
  15. 1:20–1:23 Outside The Silo
  16. 1:24–1:28 Inside The Silo
  17. 1:29–1:33 Outside Wellman Hall, looking south to Hart Hall
  18. 1:34–1:40 Back to the Arboretum
  19. 1:41–1:46 Aggie Stadium
  20. 1:47–1:52 The Pavilion
  21. 1:53–2:02 Soccer field
  22. 2:03–2:06 Dobbins Baseball field
  23. 2:07–2:11 My favorite shot...looking up from within the Death Star complex
  24. 2:12–2:20 Back to the Arboretum
  25. 2:21–2:23 Looking at the entrance to Hart Hall from corner of Shields Library
  26. 2:24–2:27 Looking at northern entrance to Mrak Hall
  27. 2:28–2:32 Dutton Hall
  28. 2:33–2:36 I think this is on East Field, behind Dutton Hall
  29. 2:37–2:40 The ARC
  30. 2:41–2:44 Looking at Peter A. Rock Hall from across the turning circle at Hutchinson Drive & California Avenue
  31. 2:45–2:48 Hmm, somewhere west of campus? Update: now confirmed to be Hopkins Road (thanks to @brendawrites)
  32. 2:49–2:53 Not sure...possibly the Teaching Vineyard next to the Robert Mondavi Institute for Wine and Food Sciences

Thanks again to Joe for making a beautiful video which serves as a wonderful advertisment for UC Davis.

 

Summary: migrating from Gmail to FastMail

I thought I would group together links to my set of six posts about how I have migrated from Gmail to FastMail:

  • In part 1, I explained the complexity of my email setup.
  • I used part 2 to talk about why I wanted to migrate away from the (admittedly very good) tools provided by Google
  • Part 3 went over the steps I took to prepare for the migration
  • Part 4 proceeded to talk about how you can copy email from Gmail to FastMail and also included some links to some other useful resources online
  • In part 5, I covered some of the specific issues that arose duing the migration (e.g. DNS configuration)
  • Finally, I used part 6 to list the good and bad things that I have experienced during (and since) this migration