Monday, March 29, 2010

Best new omics word: the beardome - absolutely brilliant

Not much to say other than that this is awesome: The Beard-ome : Oscillator: "Christina Agapakis".

Hat tip to Bora

WANTED: Used Roche GS FLX sequencer; ready to buy

Well, I have been looking around on the web for a bit and figured I should just post to my blog. We are in the market for a used Roche GS FLX sequencer. Anyone know of one for sale? We had planned to buy a new one but with the 3rd generation sequencers coming out soon it seems unwise to spend 500K on a new machine. But I like the current capabilities in the Roche GS FLX, as well as the apparently soon to be released ~1000 base pair reads. So we still would like to have the technology here at UC Davis. So if you know of one for sale, please let me know.

Sunday, March 28, 2010

Looking to open access (preferably w/ CC licenses) review papers covering introduction to phylogenetic trees and methods

I am teaching a class this spring and as part of the class am having one lecture on "Phylogenetic trees and methods." I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good?

Wednesday, March 24, 2010

And the Joint Genome Institute's User Meeting Begins (posting notes/feeds here)

Will be posting my notes and feeds (e.g., Friendfeed) here - so stay tuned if you want to hear about the JGI User Meeting

Pictures here:

FriendFeed Notes on Talks here:

Monday, March 22, 2010

CA Proposition 16: PG&E's outrageous, offensive, misleading initiative

Just heard an ad on the radio from the Vote Yes on Proposition 16 campaign here in California.  And got a heads up from a friend about it too. Just to cut to the chase before getting into detail - this initiative is horrendous and deceptive.  Here are some details 

From Ballotpedia.Org:
"The proposed constitutional amendment would require a two-thirds majority vote of local voters before a local government could:

It is being pushed by promoters as the "Californians to Protect Our Right to Vote." bill.  But really what this is a move by PG&E to help it make more money.  Some comments/questions

1. Why is the only major donor to the Vote Yes campaign PG&E?  See here for more detail on donors, where as of today the top donors are all PG&E. 

2. Every editorial I could find came out vigorously against it:

3. Not surprisingly, many other utilities have come out against this, as it clearly favors PG&E, aka the status quo.  I am not overly sympathetic to the opinions of these other utilities but it seems that the initiative is more about reducing competition than in favoring democracy.

4. One thing that really annoys me is the component of the proposition that a two-thirds majority vote will be required before local communities can change their energy plans.  To then say that this initiative is about protecting our right to vote is just absolutely offensive.  What this is a way to try and make change of any kind very very difficult.  In this day and age, with energy becoming more and more of an issue, we should have as much flexibility as possible.  What we do not need is an initiative that requires a 2/3 majority to make changes.

5. The most astonishing aspect of the proposal has been some of the words from the head of PG&E, as reported in the Mercury News
Asked why the company was sponsoring the initiative, Darbee referred to the 2006 battle in which it spent more than $11 million to prevent Davis, Woodland and West Sacramento from defecting to the Sacramento Municipal Utility District.
"So it was really a decision about could we greatly diminish this kind of activity for all going forward rather than spending $10 (million) to $15 million a year of your money to invest in this," Darbee told the shareholders. "The answer was yes."
So basically this is there way to limit the choices of cities by putting this on a statewide ballot.  In essence, whether liberal or conservative, Democrat or Republican, I can't see why anyone would support this Proposition.  A conservative could easily see this as  PG&E trying to be the big hand of government to take away taxpayer choice.  A liberal could see this as a company using their money to buy votes and prevent choice in energy usage.  I really cannot see any potential upside in this for anyone but PG&E.  Lovely

Simple solution.  Vote No on Proposition 16.  More comprehensive solution would be to actually punish PG&E for the audacity and idiocy of this measure as well as the misleading nature of all of their ads and claims about it.  Not sure how to do that but boy do they deserve it.

UC Regents 3/24 public/ustream discussion of recent "intolerance" issues

Just got this announcement:

"The UC Board of Regents, at its March 24 meeting, will hold an extended public comment period and discussion of recent incidents of campus intolerance and UC's efforts to address them.

The Office of the President will provide live streaming video of the discussion, available to members of the public and the UC community at:

The public comment period begins at 8:30 a.m., Wednesday March 24. Following that 40-minute period, President Mark Yudof, Regents Chairman Russell Gould, Interim Provost Lawrence Pitts, Senior Policy Advisor Christopher Edley and select chancellors will discuss the recent events and the actions they are taking to ensure that these types of incidents do not occur in the future.

For employees who are unable to watch the proceedings live, an archived tape will remain available at the same web address: "

Saturday, March 20, 2010

Phyloseminar.Org 3/29 Streaming talk by Jens Lagergren on Gene Family evolution

Just got his email from the organizer of Phyloseminar.Org:

On March 29th, will present Jens Lagergren speaking
on "Probabilistic analysis of gene families with respect with gene
duplication, gene loss, and lateral gene transfer." Abstract below.

NOTE: the seminar will begin at 10h PST, which is three hours earlier
than the previous seminars.

This is 13h Eastern Standard Time, 19h Central European Time, and 6h
in Christchurch and Auckland!

Here's the abstract:

Incongruences between gene trees and corresponding species trees are
common. Gene duplication, gene loss, and lateral gene transfer are
three types of evolutionary events that can cause such incongruences.
I will first describe a probabilistic process that contains standard
models of nucleotide substitutions (i.e., such that underly
probabilistic methods for phylogenetic tree reconstruction) as well as
gene duplication and gene loss. This process takes place in a given
species tree and can be used to reconstruct a gene tree for a gene
family of interest and simultaneously reconcile the gene tree with the
species tree. I will describe the algorithms available for this model
and also describe how they perform on biological data compared to
competing methods. Finally, I will describe an extension of this model
that also contains lateral gene transfer and show how it performs on
synthetic data.

Hope to see you there!

Wednesday, March 17, 2010

Bad omics word of the day: Bibliome

(Note - this was supposed to be published tomorrow but clicked the wrong button - so we will have two today - yay)

And here is a doozy.  The bad omics word of the day is ... Bibliome. See for example, the source of all knowledge (Wikipedia): Bibliome - Wikipedia, the free encyclopedia Which also refers to some other related omics words the literaturome and the textome.  Now, every one at once, 1,2, 3, groan.

Back to the bibliome which is described in Wikipedia as follows:
"The bibliome is the totality of biological text corpus. This term was coined around 2000 in EBI (European Bioinformatics Institute) to denote the importance of biological text information. 
The first uses seem to be in and around 2001. See this article from Nature Reviews Genetics in 2001 Mining the bibliome.  And another one with a very similar title in EMBO in 2002: Mining the Bibliome (with some other words in the title).  And another one in Pharmacogenomics entitled Mining the bibliome. 

And though I would have thought and hoped that it would not get used much it has shown up here and there for a while (see for example Ten thousand views of bioinformatics: a bibliome perspective.). 

So here is a question - what exactly is "the totality of biological text corpus"?  And does this thing, whatever it is, need an omics word?

Hat tip to @rdmpage and others for pointing this one out.

Bad omics word of the day: epitehliome epitheliome

The Bad Omics Word of the Day: Epitheliome. Not really much to say. See for example:

The epitheliome: agent-based modelling of the social behaviour of cells. [Biosystems. 2004 Aug-Oct] - PubMed result

Hat tip to Steve Koch on Friendfeed for this.

Tuesday, March 16, 2010

Bad omics word of the day: nutriome

And the winner is ...

From the abstract "strategies to determine dietary reference values of single micronutrients and micronutrient combinations (nutriomes)"

As with my last Bad Omics word, I have no real clue what that means. But it seems this author has been using the term for a while.

Some other papers have defined it more concisely such as "Nutriomic analysis is a postgenomic-based study of nutritious components (nutriome)."

Yuck yuck and double yuck is what I say.

Hat tip to @nutrigenomics and @larry_parnell and @eurogene for pointing this one out. 

Monday, March 15, 2010

Bad omics word of the day: transactome

Hat tip again to Rami Aziz for pointing this out on twitter

From the abstract: "The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined “transactome”)."

I have no real clue what that means.

I confess, going to skip this paper.  So I will not figure out if there is some clearer meaning. But here's a guess - the word is unnecessary.

Sunday, March 14, 2010

Bad omics word of the day: N-terminome

Yes indeed. Someone has used N-terminome.

Nature Protocols: System-Wide Proteomic Identification of Protease Cleavage Products by Terminal Amine Isotopic Labeling of Substrates

From the introduction:

"The sequence and nature of all the protein amino-termini (N-termini) within the proteome (the N-terminome) provides valuable functional annotation, since translation start sites, N-terminal isoforms, modifications and truncations determine the cellular localization, activity and fate of most proteins"

Prediction: will not get widespread use.

But they will get an award today: the Bad Omics Word of the Day.

Hat tip to @mglo for this one.

Good words on bad omics words: "A crisis in postgenomic nomenclature" from 2002

Just got pointed to a fun paper from 2002 "A Crisis in Postgenomic Nomenclature by Stanley Fields and Mark Johnston" by Mark Johnston himself. Their paper, in Science, is available for free on Stanley Fields website here. It is actually a hilarious tongue in cheek read where they proceed from arguing for more specificity in omics names (e.g., they go so far as to propose a EC# like system with things such as the "" and also that conditions should be specified like the "37°-7.4-G1-Golgi-N-but-not- 63 O-linked glycosylome".  And they end with a proposal to replace the term "the cell" with either the someone or the omesome.  It is definitely worth a read.

Saturday, March 13, 2010

Bad omics word of the day: miRNAome

Hat tip to Rami K. Aziz on Twitter for this.

The winner of today's Bad Omics Word of the Day is a paper in PLoS One: PLoS ONE: Characterization of the Melanoma miRNAome by Deep Sequencing

They even slipped the word into the title. I do not think the word was coined by them as I found some older references going back at least to 2005: MicroRNA Gene Expression Deregulation in Human Breast Cancer in Cancer Research.

Given that there were only 847 google hits as of today, the word clearly has not taken off, which is good.  But alas it is still being used, even in titles.  As far as I can tell, what they mean by the term is "All the miRNAs in a particular cancer class" --- unclear to me why that needs an ome.

Friday, March 05, 2010

Bad omics words of the day: modomics and tRNomics

Well, just was browsing through a paper on the non coding RNAs of the model halophile Haloferax volcanii, which I study. The paper BioMed Central | Full text | RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes is quite useful. However, the terminology is icky. They use two omics terms I have never seen before, but I guess should have known were out there: tRNomics (all the tRNAs in an organism, or something like that) and modomics (the pattern of RNA modifications). These are really not needed are they? And since they are both in the same paper, today we are giving out a linked "Bad omics word of the day" award to both of these terms.

Tuesday, March 02, 2010

Wildhorse Ag Buffer and Burrowing Owls

Just thought I would post some pics here from a walk on the Ag Buffer trail behind WildHorse gold course. Lots of burrowing owls out there these days.

Bad omics word of the day: variome

OK - I am back. I cannot resist. The Bad Omics Word of the Day is Variome. I am not even completely sure what people mean by this, but I guess if you want to know you can go to this meeting: 3rd HVP Meeting � Paris

On the web site the seem to define this project as an attempt to "collect variation causing disease (mutations) in all genes world wide" so I guess that is what variome means to them. So - I wonder here - what is wrong with "polymorphisms"??????

HT to @ivanoransky and @boraz for pointing this out to me (by feeding my other people's tweets).

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