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

 

Migrating From Gmail To FastMail: Part 6

Okay, so I have been negligent in finishing my series of blog posts about my Gmail to FastMail migration. But that negligence ends today.

This is my final post in this series. First, I will list the things I don’t like about FastMail and discuss the problems that I’ve had during my migration from Gmail. Then I’ll cover the things I like about FastMail.

Bad things about FastMail

The list of problems that I have experienced is almost non-existent, and the few issues I have had were my own fault! At one point in my migration, I had my Apple Mail app (on OS X) set up with both my Gmail and my new FastMail account. This meant that I effectively had duplicates of everything.

When I was trying to, ahem, ‘tidy up’ my soon-to-be-defunct Gmail account and check that everything had migrated over to FastMail properly, I accidentally deleted my Gmail ‘Spam’ folder. Only it turned out that this was actually my FastMail Spam folder.

It took me a while to troubleshoot this, but only because a lot of FastMail’s online documentation specifically refers to a folder called ‘Junk Mail’ and not ‘Spam’. E.g. (click to enlarge)

When I later noticed that I was unable to mark mail as junk on the FastMail website, I realized that I had maybe deleted the wrong folder. A quick email to FastMail confirmed that in their new web interface, they have renamed ‘Junk Mail’ to ‘Spam’. Their support team quickly rebuilt my Spam email folder and all was well again.

So that’s my sole criticism of FastMail: because of an error that was my fault I was temporarily confused by some of their documentation which is not up to date. I can live with this!

Good things about FastMail

  1. It works just as you want a mail service to work. Stable, reliable, and powerful.

  2. If you use a custom domain (as is the case for me), they set up a default subdomain at mail.yourcustomdomainname.com that lets you check your mail [1]. I found this was a nice little touch.

  3. The Desktop web app is good. Really good. Supports all of your Gmail keyboard shortcuts and many more besides.

  4. The mobile web app is also fantastic, and supports many great ‘slide’ gestures that makes it feel like a native iOS app. E.g. (click to enlarge):

  5. There is a great set of default settings (click to enlarge):

  6. But when you need them, their Advanced settings are there and they could probably keep you occupied for several days (every option in the left-sidebar opens a whole page of preferences). Click to enlarge:

  7. Fantastic, and timely, support from real people!

  8. Integration with 3rd party mail clients is straightforward and seems to work as expected.

  9. The web app has four main components: Mail, Address Book (I easily imported my addresses from OS X Contacts app), Notes (a simple way of collecting some thoughts in the style of Simplenote [2], and Files.

  10. The aforementioned file storage space can be used to host files or photo galleries.

Native or web app?

I’m really impressed by the web app experience when using FastMail. So much so, that I’m currently switching a lot between the web apps (on my Mac and on iOS) and 3rd party mail clients. FastMail is working beautifully with Apple’s mail apps (on OS X and iOS) as well as apps like the fantastic AirMail (OS X) and Triage (iOS).

Overall

I’m loving FastMail, and still discovering many new things about it every day. I’ve no regrets about migrating away from Gmail and am happy to pay a fair price for this level of quality, functionality, and service.

  1. You can, of course, still access the web mail interface at http://fastmail.fm  ↩

  2. Though there is no easy way of searching notes that I could find.  ↩

7 reasons why I don't like content 'aggregators' who scrape blog sites

Today a post on twitter drew my attention to Bioinfo-Bloggers, a site that aggregates content — i.e. the full blog post is reproduced — from 28 different bloggers who write about bioinformatics and genomics.

Outwardly, this might seem like a good idea. The bloggers get more exposure to their material, and readers can visit just one site instead of 28 separate RSS feeds. However, there are several reasons why I have issues with this type of aggregation. Many of my concerns apply even when individual bloggers have expressly licensed their material for reuse (e.g. by use of a CC0 Creative Commons license).

  1. The site lists the 28 blogs as 'contributors' and lists the blog writers as 'authors'. This strongly suggests that the people in question have consented to their material being used, even when this is not the case.
  2. Links to the original blog posts are included, but only at the end of each reproduced entry. The included text says that 'This is a syndicated post', further suggesting that the original authors agreed to have their content syndicated.
  3. The Bioinfo-Bloggers website asserts copyright over all material (see footer section of website).
  4. The original bloggers lose web traffic. This can matter for minor reasons such as when you want to include details of how popular your blog is for outreach sections on research grants. But it potentially — depending on how much traffic Bioinfo-bloggers gets — deprives you of knowing who is looking at your content, which articles are more popular, etc.
  5. People don't a chance to comment on your blog (unless they follow the links). You may lose some direct engagement with your readers.
  6. If people start using this site rather than viewing your blog, what happens if Bioinfo-Bloggers stops including your blog site, or shuts down altogether? In the former case, people might just assume you are not posting any more.
  7. What happens if Bioinfo-Bloggers starts including content from other blogs that you don't approve of? Your blog post may appear alongside another which espouses views you find offensive.

The first three points could easily be addressed by removing the claim of copyright over all material, by making it explicit that this site is just scraping other sites and that the original bloggers may not be aware of this, and by placing links to the original blog content at the top (not bottom) of each article.

There are currently some ongoing discussions about this on Twitter. E.g.

Bacon, bacon, bacon: a bacon extravaganza

Today I cooked a three course meal with every dish featuring bacon. This was a special treat for some dear friends of ours who will sadly be leaving Davis after many years here. One friend has always made it clear to us that she loves bacon, so I thought I would cook her a meal to remember.

The appetizer — for which I stupidly forgot to take a picture of — was Bacon Cheddar Deviled Eggs. The bacon was cooked on top of a wire rack in the oven (to try to reduce the fat content a little bit). I used an English mustard (Colman's) which has quite a tang. Eggs were served with a few cherry tomatoes on the side that were drizzled in olive oil and served with a large drop of a local Black Currant Balsamic Vinegar.

The main course was a bacon-wrapped cheddar and stout meat loaf (my first time ever cooking meat loaf). The organic beef was grass-fed and from a local source.

 

 

 


 


 


Accompanying the meat loaf was some mashed potatoes (which included some of the bacon fat, plus a couple of handfuls of crushed cooked bacon) and a green bean and garlic recipe that we love (you add fresh lemon zest right at the end).

 

For dessert, we did not attempt to shy away from bacon. I made some beer-candied bacon (using the same stout that went into the meat loaf) which was served on some vanilla bean ice-cream with a little bit of dark chocolate with sea salt.

 

I have never cooked so much bacon in my life! I guess I could have gone the extra step and also prepared a bacon martini but maybe that would have been too much?

 

Gmail, FastMail, and Mavericks…can't you all just get along?

As a brief interlude to my never ending series of blog posts about migrating from Gmail to FastMail, I'll quickly note that:

a) Gmail has some problems when used as an account in the Mail app of  Mac OS 10.9 (Mavericks)

b) FastMail also has some issues when being used with Mail on Mavericks (these would seem to be due to changes Apple made)

So on the one hand, the former news might encourage more people to move away from Gmail but the latter news item means that Apple's Mail app needs some fixes before being ready to work with FastMail under 10.9 (of course, web access to FastMail is unaffected). This is making me consider waiting a little while before upgrading to 10.9.

 

Update: 31st October

Turns out the 2nd item above was not FastMail's fault and was an issue with a particular user.

Update: 4th November

Marco Arment's piece on the wider issue of Gmail not adopting standard IMAP protocols is well worth a read.

Migrating from Gmail to FastMail: part 5

In this part, I will discuss the changes that I had to make to get FastMail working with my own personal domain.

When I was only using Gmail, I used a personal domain name that I had purchased from the excellent Hover domain name registrar[1]. For just $5 a year, Hover will forward email from a personal email address (using your own domain) to another email account. If I borrow from the fictional example in part 1 of this series, let’s assume I own the domain name mos-eisley-cantina.com and I was previously using Hover to forward mail to greedo@mos-eisley-cantina.com to my Gmail address (greedo_1977@gmail.com). How does this happen with FastMail?

One of the reasons I chose FastMail was that I knew that they supported personal domains[2]. You still get your own FastMail email address as well (and this becomes your account name) but I don't intend to ever use this as an email address.

On following FastMail’s guide to setting up your own domain name I was surprised to find that I had to alter my Hover name server settings for the mos-eisley-cantina.com domain name. I.e. I had to configure Hover to redirect all traffic heading towards mos-eisley-cantina.com to instead go to FastMail’s servers.

2013-10-25 at 9.34 AM.png

I thought I would just be configuring the mail settings at Hover.com rather than redirecting all traffic to FastMail. One of my concerns about this was that I was also using Hover to forward web traffic from mos-eisley-cantina.com to another domain that I own (er…let’s call it wretchedhiveofscumandvillainry.com). As soon as I changed the name server settings in Hover, this forwarding was broken.

I needn’t have worried. Turns out that FastMail provides a lot of options for custom DNS configuration. By visiting Settings->Advanced->Websites/Redirects I could configure my web traffic to be redirected just as before:

2013-10-25 at 9.44 AM.png

So I now have FastMail set up to use my custom domain, though when I set up mail clients such as Apple’s Mail app, I need to use my underlying FastMail email address[3] in the 'User Name' field. To make my custom domain name the default email account, you need to place it first in a comma separated list of email addresses in Apple Mail’s ‘Email address’ field:

2013-10-25 at 1.47 PM.png
  1. If you want to give me some Hover referral love, please use this link when signing up for a domain (I will get $5 in credit)  ↩
  2. Though you have to sign up for the more expensive enhanced plan to have this feature. On the flip side, I’m no longer paying Hover $5 a year for the email forwarding.  ↩
  3. FastMail provides many different options for your account email address with maybe 50 different domain name extensions (e.g. allmail.net, fastemail.us, myfastmail.com). I went for the default username@fastmail.fm format.  ↩

Migrating from Gmail to FastMail: part 4

I’m falling behind on my (seemingly never-ending) series of posts about migrating from Gmail to FastMail. I still have lots that I want to write about, but for this post I’ll point you towards some resources I found helpful, and will briefly discuss FastMail’s IMAP migration tool.

Resources

FastMail provides a lot of really detailed and useful help online. They appreciate that many of you will want to work with FastMail on specific desktop and mobile clients and have created different help pages to address these scenarios. E.g. here is the advice on configuring Apple’s Mail app to work with FastMail folders. Their support team are also very quick to deal with emailed requests.

Here are some guides for migration of Gmail to FastMail:

FastMail’s IMAP migration tool

If you decide that you like the free trial of FastMail and want to move to using it 100%, then you will want to bring all of your Gmail (or other email) with you. FastMail has an IMAP migration tool which worked well for me. After logging in to FastMail, navigate to your Account page and select Migrate IMAP under the ‘Maintenance’ settings.

After entering your Gmail credentials, you just let this tool run in the background. It took about 4 hours to copy all of my ~15,000 emails [1]. The best part of this is that it sends you a detailed report when it finishes.

As I mentioned in an earlier post in this series, I was initially confused because my Gmail ‘All Mail’ folder seemed to shrink by several thousand emails. But this is because Gmail — which does many non-standard things with email —counts all sent emails as part of ‘All Mail’. FastMail resolves these into separate folders.

The only hitch in this process was due to my own stupidity. I use SaneBox to pre-filter my Gmail and I needed to tell SaneBox to work with FastMail instead. Foolishly, I did this while my mail was still being imported in the background. This may or may not have been the reason why I ended up with two sets of my SaneBox folders under FastMail. This was easy to resolve though [2].

In my next post, I’ll talk about how I migrated my personal domain settings over to FastMail.

  1. It leaves all the original emails in Gmail, so there is no real risk of using this tool.  ↩

  2. SaneBox gives folders a prefix to make sure that they appear at the top of your list of folders. On Gmail it uses the ‘@’ symbol, but it turns out that different providers sort email folders differently. On FastMail, these folders use a ‘+’ sign (e.g. +SaneLater). During my email migration from Gmail, I also ended up with underscores being used. This gave me a +SaneLater and a _SaneLater folder. I simply moved the contents of _SaneLater into +SaneLater, deleted the former and everything was okay from that point. But really, don’t migrate SaneBox to FastMail until you have finished the Gmail->FastMail migration!  ↩

What's in a name? Better vocabularies = better bioinformatics?

About 7:00 this morning I was somewhat relieved because my scheduled lab talk had been postponed (my boss was not around). But we were still having the lab meeting anyway.

About 8:00 this morning, I stumbled across this blog post by @biomickwatson on twitter. I really enjoyed the post and thought I would mention in in the lab meeting. Suddently though that prompted me to think about some other topics relating to Mick's blog post.

Before I knew it, I had made about 30 slides and ended up speaking for most of the lab meeting. I thought I'd add some notes and post the talk on SlideShare.



I get very frustrated by people who rely heavily on GO term analysis, without having a good understanding of what Gene Ontology terms are, or how they get assigned to database objects. There are too many published anayses which see an enrichment of a particular GO term as some reliable indicator that there is a difference in datasets X & Y. Do they ever check to see how these GO terms were assigned? No.