A 10-step guide to party conversation for bioinformaticians

http://genomebiology.com/2013/14/1/104
Alicia Oshlack

In Australia, December and January are part of the festive season. Summer is upon us and there is the mad preparation for Christmas while catching up with friends and family at barbecues, New Year's Eve parties and January beach holidays. At some social event or other (including ones at my own research institute) I inevitably get asked what I do. Responding with 'bioinformatics' is generally met with a blank stare or, in some cases, a slight edge towards a nearby door. Therefore, recently I have been working on tailoring my response so that at the end of an evening I still have people who are, firstly, willing to talk to me and, secondly, have some insight into what I do and why I find it interesting. Here I share a step-by-step guide that has helped me to convey some concept of my work to people not involved in the field, or even in science in general, when I am asked the question: 'So, what do you do?'

R negative binomial distribution

> par(mfrow=c(5,2))
> for (i in (1:10)/10) {
+   barplot(dbinom(0:10, 10, i), main=sprintf('prob=%s',i))
+ }

R code

DESeq

http://genomebiology.com/content/supplementary/gb-2010-11-10-r106-s2.pdf

Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27.

Differential expression analysis for sequence count data.

Anders S, Huber W.

Source

European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany. sanders@fs.tum.de

Abstract

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.

PMID:

 

20979621

 

[PubMed - indexed for MEDLINE] 

PMCID:

 

PMC3218662

 

R boxplot side by side

png('out.png')
boxplot(sample(100), at=1, xlim=c(0,3))
boxplot(sample(20), at=2, add=T)
dev.off()

The key here is to set

xlim=c(0,3)

and set the positions with

at=1
at=2

and set

add=T

to the second boxplot.

R boxplot with scatter points overlayed

png('out.png')
boxplot(sample(10,100,replace=T))
points(pch=21,cex=1.5,bg='red',sample(10,10,replace=T)~rep(1,10))
dev.off()

The keypoint here is this part

~rep(1,10)

So you need to associate a factor with your points!

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

http://genomebiology.com/2010/11/7/R72

Abstract

Background

Long considered to be the building block of life, it is now apparent that protein is only one of many functional products generated by the eukaryotic genome. Indeed, more of the human genome is transcribed into noncoding sequence than into protein-coding sequence. Nevertheless, whilst we have developed a deep understanding of the relationships between evolutionary constraint and function for protein-coding sequence, little is known about these relationships for non-coding transcribed sequence. This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases.

Results

Here, we performed a multi-disciplinary study of four highly conserved and brain-expressed transcripts selected from a list of mouse long intergenic noncoding RNA (lncRNA) loci that generally show pronounced evolutionary constraint within their putative promoter regions and across exon-intron boundaries. We identify some of the first lncRNA orthologs present in birds (chicken), marsupial (opossum), and eutherian mammals (mouse), and investigate whether they exhibit conservation of brain expression. In contrast to conventional protein-coding genes, the sequences, transcriptional start sites, exon structures, and lengths for these non-coding genes are all highly variable.

Conclusions

The biological relevance of lncRNAs would be highly questionable if they were limited to closely related phyla. Instead, their preservation across diverse amniotes, their apparent conservation in exon structure, and similarities in their pattern of brain expression during embryonic and early postnatal stages together indicate that these are functional RNA molecules, of which some have roles in vertebrate brain development.

4 ways to make Google Chrome use less memory

http://downloadsquad.switched.com/2010/03/31/reduce-save-conserve-memory-google-chrome/

Academic pay lagging

http://www.nature.com/nature/journal/v493/n7433/full/nj7433-567c.html?WT.ec_id=NATURE-20130124 
 
Early-career scientists with full-time jobs in US academia earn an average of US$58,000 annually, less than those in industry, non-profit or government, says a report from the US National Science Foundation (NSF). Industry pays the most: $100,000 per year in early career, and $130,000 for those 10 years past their PhDs. Academics who got a doctorate a decade ago or more earn$93,000 a year on average. Daniel Foley, a statistician for the NSF in Arlington, Virginia, says that the data underscore the need to train researchers for work outside academia.

Big data

http://www.nature.com/nature/journal/v493/n7433/full/493473a.html?WT.ec_id=NATURE-20130124

To get the best out of big data, funding agencies should develop shared tools for optimizing discovery and train a new breed of researchers, says Chris A. Mattmann.

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks

http://nar.oxfordjournals.org/content/41/2/e35.full

Abstract

More and more evidences demonstrate that the long non-coding RNAs (lncRNAs) play many key roles in diverse biological processes. There is a critical need to annotate the functions of increasing available lncRNAs. In this article, we try to apply a global network-based strategy to tackle this issue for the first time. We develop a bi-colored network based global function predictor, long non-coding RNA global function predictor (‘lnc-GFP’), to predict probable functions for lncRNAs at large scale by integrating gene expression data and protein interaction data. The performance of lnc-GFP is evaluated on protein-coding and lncRNA genes. Cross-validation tests on protein-coding genes with known function annotations indicate that our method can achieve a precision up to 95%, with a suitable parameter setting. Among the 1713 lncRNAs in the bi-colored network, the 1625 (94.9%) lncRNAs in the maximum connected component are all functionally characterized. For the lncRNAs expressed in mouse embryo stem cells and neuronal cells, the inferred putative functions by our method highly match those in the known literature. 

1. Nucl. Acids Res. (2013) 41 (2): e35. doi: 10.1093/nar/gks967 First published online: November 5, 2012

From single splicing events to thousands: the ambiguous step forward in splicing research

http://bfg.oxfordjournals.org/content/12/1/3.full.pdf+html

Emanuele Buratti, Marco Baralle and Francisco E. Baralle
Advance Access publication date 18 November 2012

Abstract
Since the discovery of RNA splicing in 1977 the knowledge of this important biological process has increased steadily  following the identification of many of the mechanistic features of splicing: from the basic cis-acting splicing signals,  through the detail composition and dynamics of the spliceosome, to the role played by accessory splicing factors  and their interactions. Moreover, the realization that most genes undergo alternative splicing has had a strong  impact in the overall cell proteome and metabolism research fields and also in better appraising the fundamental  role played by splicing defects in human disease. This robust growth of knowledge is due in particular to the development of new powerful technical tools that range from methodologies useful to focus on single events in extreme  detail to microarray and high-throughput RNA sequencing approaches that aim at providing a global vision of splicing changes. Here, we will discuss how these techniques relate to each other in terms of their  respective strengths  and weaknesses. In particular, we will focus on their value for evaluating the biological significance of splicing  events. Finally, we provide some views on how these methodologies should move forward to improve our basic  and applied knowledge of RNA splicing.

Keywords: RNA splicing; RT^PCR; Minigene; RNAseq; CLIP; splicing arrays

Songza - music playlists

http://songza.com/listen/acoustic-bedtime-songza/

Blistered Shishito Peppers

http://www.worthmysalt.com/?p=111

I ate them every chance I had that trip, eventually also discovering pimientos de Padrón, which are similar to Guernicas, but with with an occasional spicy-hot one in the mix. Eating them is a little like playing a pepper version of Russian Roulette — you never know who’s going to get the kicker until he’s reaching for more sangria.

How big is space?

http://www.bbc.com/future/story/20120321-how-big-is-space

PS2 Coop games

Baldur's Gate: Dark alliance
Baldur's Gate: Dark alliance 2
Tales of the Abyss (coop at battle only)
Champions of Norrath: Realms of EverQuest
Champions: Return to Arms
Mystic Heroes  
X-Men Legends 2: Rise of Apocalypse
Marvel : Ultimate Alliance gameplay co-op
Dynasty Warriors 4
Star Wars Battlefront
Star Wars Battlefront II
Neo Contra
The Legend of Spyro: Dawn of the Dragon
Ratchet: Deadlocked
ONIMUSHA: DAWN OF DREAMS
Gauntlet Seven Sorrows
Warriors Orochi 2
Justice League Heroes
tales of symphonia (coop at battle only)
ff9 (coop at battle only)
Tenchu: Wrath of Heaven
Marvel Ultimate Alliance
Guitar Hero
Gauntlet Seven Sorrows

http://ca.ign.com/articles/2010/05/07/the-best-ps2-co-op-games


http://www.co-optimus.com/system/6/playstation-2.html


http://www.cheapassgamer.com/forums/showthread.php?t=183288


The best coop games for the PS2 are Hack n’ Slash (so if you don't like hack n' slash you are probably out of luck):
Baldur’s Gate Dark Alliance 1 and 2 (the most fun)
Champions of Norrath/Return to Arms (fun)
The Dynasty Warriors/Samurai Warriors games (fun)
Star Wars Legos I&II (fun)
Mortal Kombat: Shaolin Monks (fun)
Xmen Legends I & II (unopened on shelf)
Hunter Wayward (not fun)

FPS coops:
Timesplitters Future Perfect (the best) and Timesplitters 2 (fun)
Darkwatch (fun)
Half Life (includes a few missions called Decay which are coop) (OK)
Medal of Honor: Rising Sun (OK)
Rainbow Six 3 (not my favorite)
Delta Force Black Hawke Down (haven’t played it enough to form an opinion)

Stealth coops:
Splinter Cell Chaos theory and Double Agent (fun).

Horror coops:
Obscure and Obscure 2 (fun when playing coop)

Platformer coops
Tak the Great JuJu Challenge (fun)
Cookies and Cream (fun)
Wallace & Grommit Curse of the Wererabbit (not as bad as it sounds)
Avatar the Burning Earth (really bad game).

Snowshoe - Atlas and MSR and Tubbs

 Good: Atlas and MSR and Tubbs

Yukon Charlie - only for introductory

http://www.morcmtb.org/forums/showthread.php?24423-Whos-got-the-best-snowshoes

View Poll Results: Which Brand is best ? what do you have ?

Voters

 

29. You may not vote on this poll

• Tubbs
  724.14%
• Atlas
  517.24%
• Redfeather
  310.34%
• Yukon Charlies
  00%
• Classic Wood Framed
  620.69%
• Other
  827.59%

http://www.mec.ca/AST/ShopMEC/MemberPicks/Snowsports/PRD~5022-680/msr-evo-22-unisex.jsp 

MSR Evo 22 (Unisex) $139.00 CAD