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.

New JABBA awards for crimes against bioinformatics acronyms

JABBA is an acronym for Just Another Bogus Bioinformatics Acronym. I hand out JABBA awards to bioinformatics papers that reach just a little bit too far when trying to come up with acronyms (or intialisms). See details of previous winners here.

So without further delay, let's see who the new recipients are. As always, journals like Bioinformatics produce many strong candidates for JABBA awards. Here are three winners from the latest issue:

  1. mpMoRFsDB: a database of molecular recognition features in membrane proteins - What is it with the need for so much use of mixed-case characters these days? It makes names harder to read, and this database has a name which doesn't really roll off the tongue.
  2. CoDNaS: a database of conformational diversity in the native state of proteins - More mixed case madness. I'm really unsure how this database should be pronounced. 'Cod Naz'? 'Code Nass'? 'Coe Dee-en-ays'? The abstract suggests that the acronym stems from the name 'Conformational Diversity of Native State', so I guess we should be thankful that they avoided the potential confusion of naming this database 'CoDoNS'.
  3. GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks - If you want your bioinformatics tool to have a cool sounding name, just give it that name. Don't feel that you somehow have to tenuously arrive at that name from a dubious method of selecting just the letters that make it work. The abstract of this paper reveals that GALANT stems from 'GrAph LANdscape VisualizaTion'. So the full name only consists of three words, and the initial letter of one of those words doesn't even make it into the acronym/initialism. They may as well call their tool 'GREAT' (GRaph landscapE visualizATion).

The joys of dealing with well-annotated 'reference' genomes

Important update included at bottom of this post

Arabidopsis thaliana has one of the best curated eukaryotic genome sequences so you might expect working with Arabidopsis data to be a joy? Well, not always. Consider gene AT1G79920. This gene has two coding variants (AT1G79920.1 and AT1G79920.2) which only seem to differ in their 5' UTR regions:

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The primary source for Arabidopsis genome information is The Arabidopsis Information Resource (TAIR) but another site called Phytozome has started collating all plant-related genome data (often pulling it from sites like TAIR).

Both sites allow you to download coding sequences for each gene from their FTP sites, or view the same sequence information on their web sites. You could also download GFF files and using the coordinate information, extract the coding sequences from the whole genome sequence.

A simple sanity check when working with coding sequences is that the length of a coding sequence should be divisible by 3 otherwise there might be a frameshift. There seems to be an issue with AT1G79920 in that it sometimes has a frameshift. I say sometimes because it depends on where you look at the data.

Here is a sequence alignment for exons 5 and 6 of both coding variants of this gene. The sequence identifiers include a 'P' or 'T' to indicate whether the information came from Phytozome or TAIR and they also denote whether it was taken from their web or FTP site. I also insert 'gtag' into one sequence to illustrate where the intron between these exons would occur.

2013-08-30 at 3.25 PM.png

The first boxed rectangle highlights a base that looks like a SNP, but these are coding variants with UTR variation, so the underlying genome sequence in the coding regions should be identical.

The second box is perhaps more disturbing. The web site versions of exon 7 all have a 1 bp deletion which would lead to a frameshift. I guess this error started at TAIR and propagated to Phytozome, but the fact that both sites also have a correct version available on their FTP site is confusing and troubling.

My boss first discovered this by looking at the GFF files for the Arabidopsis genome and this was one of 25 genes with a 'not-divisible-by-3' length error. So it pays to always check — and double check — your data.

Time to send an email to TAIR and Phytozome to report this.

Update

I heard back from TAIR and Phytozome and it seems that there are a small number of likely genome sequence errors in the latest (TAIR10) release of the A. thaliana genome. When these affect genes and would introduce a frameshift error, TAIR make manual edits to the resulting files of CDSs, transcripts, and proteins. They do this when there is clear homology from genes in other species that suggests the change should be made.

So if you work with downloaded FASTA files from the FTP site, you won't see these errors. If you work from GFF files (which is presumably what some of their web displays do), you'll run into these issues. There is a small file (TAIR10sequenceedits.txt) included as part of the TAIR10 release which documents these changes.

Thanks to a speedy and helpful response from both sites. Perhaps I should retitle this post The Joys of Dealing with Fast and Knowledgable Genome Curators?

Crappy science spam from Photon Journals

I've started receiving more and more science-related spam recently. Some of these are semi-legitimate, like those from the OMICS group, but should still be avoided (here's a good cautionary tale of what to expect if you go to an OMICS Group conference).

Sometimes I'm just disappointed by how little effort these spammers take to make their emails looks professional. Over the last couple of weeks I've received four emails from 'Photon Journals' asking me to submit my research to some of their (many) journals. To give you an idea of how lame their attempts at spamming people are, consider that:

  1. Their email comes from a Hotmail account.
  2. They address me as 'Dear Dr. Krbradnam' (clearly they have phished my academic email address from somewhere and just assumed that this is my surname).
  3. Their email is written in purple!
  4. Two emails on the same day ask me to submit material to two completely different journals (see below).
  5. The 'website' for the journal is hosted on Google Sites
  6. The website looks like it was designed by a five year old on acid (see below).
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The modus operandi of these fake journals is just to charge you to submit your paper (and really it can be any paper, no-one is going to check it, let alone read it). I guess we should be grateful that some of these are so obviously fake, that it makes it easier to ignore them. Several sites are now collating list of all of these bogus journals (there are a lot).