Blog Index
The journal that this archive was targeting has been deleted. Please update your configuration.

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:

I will leave the original posts here (possibly adding redirect links) but 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 about me, living in Davis, working at UC Davis etc.


Paper review: anybody who works in bioinformatics and/or genomics should read this paper!

I rarely blog about specific papers but felt moved to write about a new paper by Jonathan Mudge, Adam Frankish, and Jennifer Harrow who work in the Vertebrate Annotation group at the Wellcome Trust Sanger Institute.

Their paper, now out in Genome Research, is titled: Functional transcriptomics in the post-ENCODE era.

They brilliantly, and comprehensively, list the various ways in which gene architecture — and by extension gene annotation — is incredibly complex and far from a solved problem. However, they also provide an exhaustive description of all the various experimental technologies that are starting to shine a lot more light on this, at times, dimly lit field of genomics.

In their summary, they state:

Modern genomics (and indeed medicine) demands to understand the entirety of the genome and transcriptome right now

I'd go so far as to say that many people in genomics assume that genomes and transcriptomes are already understood. I often feel that too many people enter this field with false beliefs that many genomes are complete and that we know about all of the genes in this genomes. Jonathan Mudge et al. start this paper by firmly pointing out that even the simple question of 'what is a gene?' is something that we are far from certain about.

Reading this paper, I was impressed by how comprehensively they have reviewed the relevant literature, pulling in numerous examples that indicate just how complex genes are, and which show that we need to move away from the very protein-centric world view that has dominated much of the history of this field.

LncRNAs, microRNAs, and piwi-interacting RNAs are three categories of RNA that you probably wouldn't find mentioned anywhere in text books from a decade ago, but which now — along with 'traditional' non-coding RNAs such as rRNAs, tRNAs, snoRNAs etc. — probably outnumber the number of protein-coding genes in the human genome. Many parts of this paper tackle the issue of transcriptional complexity, particularly trying to address the all-important question how much of this is functional?

I found that so many parts of this paper touched on previous, current, and possible future projects in our lab. Producing an accurate catalog of genes, understanding alternative splicing, examining the relationship between mRNA and protein abundances, looking for conservation of signals between species...these are all topics that are near and dear to people in our lab.

Even if you have no interest in the importance of gene annotation — and shame on you if that is how you feel — this paper also serves as a fantastic catalog of the latest experimental techniques that can be used to capture and study genes (e.g. CAGE, ribosome profiling, polyA-seq etc).

If you have ever worked with a set of genes from a well curated organism, spare a thought for the huge amount of work that goes into trying to provide those annotations and keep them up to date. I'll leave you with the last couple of sentences from the paper...please repeat this every morning as your new mantra:

Finally, no one knows what proportion of the transcriptome is functional at the present time; therefore, the appropriate scientific position to take is to be open-minded. We thus do not claim that the annotation of the human genome is close to completion. If anything, it seems as if the hard work is just beginning.


More JABBA awards for inventive bioinformatics acronyms

A quick set of new JABBA award recipients. Once again these are drawn from the journal Bioinformatics.

  1. NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data - the mixed capitalization of this software tool is a little uneasy on the eye. But more importantly, a Google search for 'netweavers' returns lots of links about something entirely different. I.e. NetWeavers (and NetWeaving) is already a recognized term in another field.
  2. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. - the 3 part of this algorithm's name is deliberately written in superscript by the authors. This implies 'cubed', but I think it is really referring to 3 lots of 'M' related words because the full name of the algorithm is 'Gene Inactivation Moderated by Metabolism, Metabolomics and Expression'. GIM3E is not something that is particularly easy to say quickly, though it is much more Google friendly than NetWeavers.
  3. INSECT: IN-silico SEarch for Co-occurring Transcription factors - making an acronym into the name of a plant or animal name is quite common in bioinformatics. A couple of examples are worth mentioning. There is the MOUSE resource (Mitochondria and Other Useful SEquences) and also something called HAMSTeRS (the Haemophilus A Mutation, Structure, Test and Resource Site). The main problem with acronyms like these is that they can be to hard to find using online search tools (e.g. Google for hamster resources). A secondary issue is that the name just doesn't really connect to what the resource/database/algorithm is about. The INSECT database contains information about 14 different species, only one of which is an insect.

I'll no doubt be posting again the next time I come across some more dubious acroynms.


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