gene|fish

TRYING TO UNDERSTAND MY OLD SPREADSHEETS

Wed, 22 May 2013 11:13:28 -0700

credit: Capecodnative

Map of Life

Tue, 21 May 2013 11:00:16 -0700

By bringing together all types of information about species distributions, providing model-based integration, and providing a system for users to build upon our knowledge, the Map of Life project hopes to support our community in understanding and saving the world’s biodiversity.

There is now a demo release of Map of Life!

This demo allows you to map and produce list of species anywhere for ~ 46,000 species (includingall described birds, mammals and amphibians - for info check the ‘Dashboard’).

Map species distributions : Type species name in ‘Search’ window, select layer source and type. Use controls on top left and right of screen. Video .

Below is a screenshot of an Ostrea lurida search. (There is tons of Crassostrea data too!)

via Tidal Cycles - oystergen.es http://bit.ly/159Htqv

Mac Experiments with Spiders

Tue, 21 May 2013 09:53:33 -0700

Mac Experiments with Spiders

Scholar Alert: New citation

Mon, 20 May 2013 17:44:35 -0700

Scholar Alert: New citations to my articles

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

A Albaina, M Iriondo, I Velado, U Laconcha… - Animal Genetics, 2013

Summary The optimal management of the commercially important, but mostly over-
exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna
(BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure …

Poly I: C induces a protective antiviral immune response in the Pacific oyster ( Crassostrea gigas) against subsequent challenge with Ostreid herpesvirus ( …

TJ Green, C Montagnani - Fish & Shellfish Immunology, 2013

Abstract In-vivo studies were carried out to investigate the protective effect of a synthetic viral
analogue (poly I: C) against Ostreid herpes virus (OsHV-1 Î¼var). Pacific oysters (Crassostrea
gigas) were immune-primed by intramuscular injection of 240 Î¼g of poly I: C or sterile …

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Ever hear of Nostrasamus?

Mon, 20 May 2013 13:19:59 -0700

That’s not a typo. Of course everyone’s heard of that old fool Nostradamus, who was supposed to be able to predict the fate of the world (including the OJ Simpson trial!). However, I think he’s a miserable failure.

NostraSAMus (that refers to me, by the way), on the other hand, seems to actually have a good grasp on reality and the future. As reference, notice what I wrote in this 2007 Genefish post (my first post to the lab blog, in fact!): “Soon, I’m sure we’ll all be able to buy personal GPS units so that we’ll be able to post our real-time locations on Google Earth/Maps and setup an RSS feed for our blogs without having to even be at a computer. Hmmm, maybe I should get that idea notarized/patented…”

Now, another question is whether I was being sarcastic (I’m never sacastic, though [/sarcasm]) or, more likely, an amazing visionary who can see into the future. I suspect the latter (just for reference, the first iPhone wouldn’t be released until a full year after that post).

Anyway, now that I’m done fluffing my ego, I was simply reminiscing about the lab and this blog a bit and I stumbled across that amazing post from 6 years ago. Granted, I, of course, knew that I’d still be working in the lab 6 years from when I started in March 2007. You can even ask Steven what my response was to his interview question of:

SR - “Where do you see yourself in 5yrs?”

My response: “Celebrating the 5yr anniversary of you asking me that question.” (Thank you, Mitch Hedberg!)

Despite my predictive abilities, I never envisioned how the lab would evolve over these last 6 years. We started out with skyscrapers of yeast plates:

Moved on to octopus eggs:

Continued with lab “jokes”

Acquired some new personnel:

The big boss man got tenured (and he’s happy about it)!

And we’ve finally settled on bioinformatics as our lab activity of choice. We’ve had to dive head first into the world of big data acquisition, manipulation and visualization. And, as a small lab, dealing with big data sets (e.g. 120 million sequences from a single sample) has been a fun, enlightening, and frustrating learning experience. This is all particularly true since all of us our bench-trained biologists, have little-to-no “programming” experience, and are trying to discover (and rely upon) free-ware for all of this. We’ve been utilizing software like:

SQLShare - A web-based way to use SQL (good for manipulating/joining enormous tables together) without having to deal with the backend stuff, like schema and other weird tech jargon we don’t grasp.

R - Programming language geared towards data analysis (statistical) and visualization. Think command line. Ugh. R Studio is a nice “skin” that provides a nicer GUI for R.

Galaxy - A web-based means of analyzing virtually any type of “-omics” data, including basic manipulation of text files, FASTA files, BED files, etc. Has a variety of high-throughput sequencing analysis tools, too.

iPlant Discovery Environment - Similar to Galaxy but their servers are much, much faster at virtually everything. And, they also have de novo assembly software built-in (like SOAPdenovo, Trinity, and Velvet), which Galaxy does not.

BS Map - For analyzing bisulfite-treated sequences.

iPython - A notebook for tracking your programming codes that allows you to execute the codes directly in the notebook.

Integrated Genomics Viewer (IGV) - For visualizing various features annotated within a given nucleotide/protein sequence.

There are others that we have tried (and continue to try) that often serve a fringe purpose and there are others that we’d like to continue using that we just need more time using and practicing. Unfortunately, time is probably one of the most precious commodities in the lab and it’s difficult to set aside serious chunks of time to really learn, and apply, tools like Perl, Python, BioPerl, BioPython, Quadrigram, and Orange Canvas. We know these tools are immensely powerful and useful, but it’s hard to sit at the computer learning these things from the beginning while your data is just sitting around waiting to be dealt with in some fashion.

Additionally, in order to handle all this data, we’ve purchased our own server! Keeping with a trend of computer naming in the lab (most of our computers are named after birds, which should be obvious, since we do all of our work on shellfish), we call it The Eagle. It’s a Synology DS413 and it’s been one of the best purchases the lab has ever made. It has (temporarily) resolved multiple issues:

- Data storage capacity (8TB!)

- Automated “backup” (RAIDed hard drives ensure that when one HDD fails, we don’t lose any data)

- Data hosting for generating URLs for our files. Additionally, the Synology also helps to replace Dropbox, which the sizes of our data had finally outgrown.

- Direct downloads to the server eliminate the need to download large files to a desktop, only to then upload them to the server.

All in all, the last 6yrs have been pretty awesome over here in Fisheries Teaching & Research at the University of Washington. The lab is never short on exciting new work and approaches to science. Plus, we really have had (and continue to have) great people in the lab (personality-wise and scientific-mind-wise), which is critical to a fun, stimulating, creative laboratory.

Well, enough of the brown nosing. Time for you grad students to stop wasting time reading this blog and get back to work!

In the mean time, I think I’ll walk up to Big Time for lunch and a beer before I leave early today to play softball…

Noam Ross | Setting up Automated Reprint Requests in Gmail

Sun, 19 May 2013 11:00:22 -0700

Noam Ross | Setting up Automated Reprint Requests in Gmail

scishow: Gluten What’s the problem with gluten? Gluten is a...

Sat, 18 May 2013 11:00:14 -0700

scishow:

Gluten

What’s the problem with gluten? Gluten is a sticky protein composite found in cereal grains. Hank gives us some insight into the importance of gluten in history, as well as its impact on health in our own time.

Like SciShow? Want to help support us, and also get things to put on your walls, cover your torso and hold your liquids? Check out our awesome products over at DFTBA Records: http://dftba.com/artist/52/SciShow

References for this episode can be found in the Google document here: http://dft.ba/-5E72

Scholar Alert: New citation

Fri, 17 May 2013 18:14:44 -0700

Scholar Alert: New citations to my articles

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

Q Jiang, Q Li, H Yu, LF Kong - Genes & Genomics

Abstract Selective breeding often produces an improvement in phenotype. Much of the
phenotypic change within a species is a consequence of genetic variation. However, there is
growing evidence for phenotypic change even in the absence of DNA sequence …

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an-amalgam: jellyfish madness by Alexander Semenov

Fri, 17 May 2013 11:00:14 -0700

an-amalgam:

jellyfish madness

by Alexander Semenov

Audio

Fri, 17 May 2013 09:00:18 -0700

poeposts: Find out more about the ‘Food Exploration’ Community...

Thu, 16 May 2013 11:00:07 -0700

poeposts:

Find out more about the ‘Food Exploration’ Community in the new Mercer Court buildings - launching in autumn 2013! [link for more information]

WHEN MY PI CHALLENGES ME

Wed, 15 May 2013 11:00:19 -0700

whatshouldwecallgradschool:

jtotheizzoe: Turn Your Smartphone Into A Microscope This...

Tue, 14 May 2013 11:00:03 -0700

jtotheizzoe:

Turn Your Smartphone Into A Microscope

This morning I played around with a pretty cool trick. You can turn your smartphone camera into a “microscope” of sorts using a tiny water droplet! I used my fingertip to place a droplet of water over the outer glass of my iPhone lens, juuuuust small enough to cover the glass and be held on by surface tension. Then just hold something up really close to the lens! It works in video or still mode, and I found that having the light on can help.

I chose to investigate a very small and very well preserved Tyrannosaur that I dug up.

I don’t think I need to tell you to BE CAREFUL and don’t hold me responsible if you get water in your phone. Just a dab’ll do ya. Also, best not to mention this to anyone at Ye Olde Smartphone Shoppe, or wherever you buy your gear.

Show me what you zoom in on!!

Scholar Alert: New citation

Mon, 13 May 2013 17:14:18 -0700

Scholar Alert: New citations to my articles

A resource of genomeâwide singleânucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

JM Pujolar, MW Jacobsen, J Frydenberg, TD Als… - Molecular Ecology …, 2013

Abstract Reduced representation genome sequencing such as restriction-site-associated
DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of
single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated …

Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats

SD Cardoso, D GonÃ§alves, JI Robalo, VC Almada… - Marine Genomics, 2013

Abstract Transcriptome data are a good resource to develop microsatellites due to their
potential in targeting candidate genes. However, developing microsatellites can be a time-
consuming enterprise due to the numerous primer pairs to be tested. Therefore, the use of …

Immunological responses of the mangrove oysters Crassostrea gasar naturally infected by Perkinsus sp. in the Mamanguape Estuary, ParaÃba State ( …

Abstract Perkinsus genus includes protozoan parasites of marine mollusks, especially
bivalves. In the last four years, this parasite has been detected in mangrove oysters
Crassostrea rhizophorae and C. gasar from the Northeastern region of Brazil. Hemocytes …

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jtotheizzoe: Another great track from evolutionary rapper Baba...

Mon, 13 May 2013 11:00:11 -0700

jtotheizzoe:

Another great track from evolutionary rapper Baba Brinkman

mucholderthen: At the online Library of the Japanese...

Sun, 12 May 2013 11:00:23 -0700

mucholderthen:

At the online Library of the Japanese Diet:
images of antique natural history illustrations

NATURAL HISTORY IN JAPAN: Clam / Oysters
Edo (江戸時代) a/k/a Tokugawa period (徳川時代) 1603 - 1868

source: Japanese National Diet Library’s images of natural history
also: by categories

[ via ]

Photo

Sat, 11 May 2013 11:00:21 -0700

hanspetermeyer: It’s #shellfish break time in Canada’s #oyster...

Fri, 10 May 2013 11:00:11 -0700

hanspetermeyer:

It’s #shellfish break time in Canada’s #oyster capital … #localfood (at Fanny Bay, BC)

Mac's May Goals

Fri, 10 May 2013 10:29:54 -0700

This month I am revising my MBDbs-seq data from C. gigas gill tissue. We’ve mapped the bisulfite reads to the WHOLE darn genome and so now I’m in the process of characterizing what regions of the genome are methylated in the gill tissue. Beyond that I am working on finding the best way to visualize and analyze the relationships between methylation within genes (where most of the methylation is found) and different attributes of these genes including length, number of exons, expression levels etc. Since the reads have been mapped to the WHOLE darn genome, this is the most comprehensive analysis to date and will hopefully find itself written up and submitted as a manuscript. My goal for the end of May is to have beautiful figures ready for this paper.

I am still waiting for data from Nanostring and will also be isolating DNA/RNA from the EE2 exposures for MBD-ChIP analysis.

gene|fish

TRYING TO UNDERSTAND MY OLD SPREADSHEETS

Map of Life

Mac Experiments with Spiders

Scholar Alert: New citation

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

Poly I: C induces a protective antiviral immune response in the Pacific oyster (< i> Crassostrea gigas</i>) against subsequent challenge with Ostreid herpesvirus ( …

Ever hear of Nostrasamus?

Top 20 Articles (related to: Immune response and mechanical stress susceptibility in diseased oysters)

Noam Ross | Setting up Automated Reprint Requests in Gmail

scishow: Gluten What’s the problem with gluten? Gluten is a...

Scholar Alert: New citation

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

an-amalgam: jellyfish madness by Alexander Semenov

Audio

poeposts: Find out more about the ‘Food Exploration’ Community...

WHEN MY PI CHALLENGES ME

jtotheizzoe: Turn Your Smartphone Into A Microscope This...

Scholar Alert: New citation

A resource of genomeâwide singleânucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats

Immunological responses of the mangrove oysters< i> Crassostrea gasar</i> naturally infected by< i> Perkinsus</i> sp. in the Mamanguape Estuary, ParaÃba State ( …

jtotheizzoe: Another great track from evolutionary rapper Baba...

mucholderthen: At the online Library of the Japanese...

Photo

hanspetermeyer: It’s #shellfish break time in Canada’s #oyster...

Mac's May Goals

gene|fish

TRYING TO UNDERSTAND MY OLD SPREADSHEETS

Map of Life

Mac Experiments with Spiders

Scholar Alert: New citation

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

Poly I: C induces a protective antiviral immune response in the Pacific oyster (< i> Crassostrea gigas</i>) against subsequent challenge with Ostreid herpesvirus ( …

Ever hear of Nostrasamus?

Top 20 Articles (related to: Immune response and mechanical stress susceptibility in diseased oysters)

Noam Ross | Setting up Automated Reprint Requests in Gmail

scishow: Gluten What’s the problem with gluten? Gluten is a...

Scholar Alert: New citation

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

an-amalgam: jellyfish madness by Alexander Semenov

Audio

poeposts: Find out more about the ‘Food Exploration’ Community...

WHEN MY PI CHALLENGES ME

jtotheizzoe: Turn Your Smartphone Into A Microscope This...

Scholar Alert: New citation

A resource of genomeâwide singleânucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats

Immunological responses of the mangrove oysters< i> Crassostrea gasar</i> naturally infected by< i> Perkinsus</i> sp. in the Mamanguape Estuary, ParaÃ­ba State ( …

jtotheizzoe: Another great track from evolutionary rapper Baba...

mucholderthen: At the online Library of the Japanese...

Photo

hanspetermeyer: It’s #shellfish break time in Canada’s #oyster...

Mac's May Goals

A resource of genomeâwide singleânucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Immunological responses of the mangrove oysters< i> Crassostrea gasar</i> naturally infected by< i> Perkinsus</i> sp. in the Mamanguape Estuary, ParaÃba State ( …