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This Winter Storm Could Make It Into Coastal Flood Record Books - WXshift

Featured News - Wed, 01/20/2016 - 12:00
Coastal flooding is a major concern as a major winter storm heads for the East Coast this weekend. Lamont-Doherty's Adam Sobel discusses what goes into a storm surge and why the risk is high.

Mystery Beneath the Ice - PBS NOVA

Featured News - Wed, 01/20/2016 - 12:00
What’s behind the death of a tiny creature with an outsized role in the Antarctic? Lamont-Doherty's Hugh Ducklow and his team at Palmer Station take a PBS camera crew beneath the ice.

2015 Officially the Warmest Year on Record - Mashable

Featured News - Wed, 01/20/2016 - 12:00
NOAA and NASA confirm that 2015 was the warmest year on record. Lamont-Doherty's Jason Smerdon calls the record alarming but not surprising. "The trend has been predicted for decades, and all the consequences associated with it have been predicted, as well," he said.

Installing paprica on Mac OSX

Chasing Microbes in Antarctica - Wed, 01/20/2016 - 09:55

The following is a paprica installation tutorial for novice users on Mac OSX (installation is Linux is quite a bit simpler). If you’re comfortable editing your PATH and installing things using bash you probably don’t need to follow this tutorial, just follow the instructions in the manual. If command line operations stress you out, and you haven’t dealt with a lot of weird bioinformatics program installs, use this tutorial.

Please note that this tutorial is a work in progress.  If you notice errors, inconsistencies, or omissions please leave a comment and I’ll be sure to correct them.

paprica is 90 % an elaborate wrapper script (or set of scripts) for several core programs written by other groups. The scripts that execute the pipeline are bash scripts, the scripts that do that actual work are Python. Therefor you need to get Python up and running on your system. The version that came with your system won’t suffice without heavy modification. Best to use a free third-party distro like Anaconda (preferred) or Canopy.  If you already have a mainstream v2.7 Python distro going just make sure that the biopython, joblib, and pandas modules are installed and you’re good to go.

If not please download the Anaconda distro and install it following the developer’s instructions. Allow the installer to modify your PATH variable. Once the installation is complete update it by executing:

conda update conda conda update --all

Then you’ll need to install biopython, joblib, and pandas:

conda install biopython conda install joblib conda install pandas

In case you have conflicts with other Python installations, or some other mysterious problems, it’s a good idea to test things out at this point. Open a shell, type “Python”, and you should get a welcome message that specifies Anaconda as your distro. Type:

import Bio import joblib import pandas

If you get any error messages something somewhere is wrong. Burn some incense and try again. If that doesn’t work try holy water.

One challenge with paprica on OSX has to do with the excellent program pplacer. The pplacer binary for Darwin needs the Gnu Scientific Library (GSL), specifically v1.6 (at the time of writing). You can try to compile this from source, but I’ve had trouble getting this to work on OSX. The easier option is to use a package manager, preferably Homebrew. This means however, that you have to marry one of the OSX package managers and never look back. Fink, Macports, and Homebrew will all get you a working version of GSL. I recommend using Homebrew.

To download Homebrew (assuming you don’t already have it) type:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Follow the on-screen instructions. Once it is downloaded type:

brew install GSL

This should install the Gnu Scientific Library v1.6.

Assuming all that went okay go ahead and download the software you need to execute just the paprica_run.sh portion of paprica. First, the excellent aligner Infernal. From your home directory:

curl -O http://selab.janelia.org/software/infernal/infernal-1.1.1-macosx-intel.tar.gz tar -xzvf infernal-1.1.1-macosx-intel.tar.gz mv infernal-1.1.1-macosx-intel infernal

Then pplacer, which also includes Guppy:

curl -O https://github.com/matsen/pplacer/releases/download/v1.1.alpha17/pplacer-Darwin-v1.1.alpha17.zip unzip pplacer-Darwin-v1.1.alpha17.zip mv pplacer-Darwin-v1.1.alpha17 pplacer

Now comes the tricky bit, you need to add the locations of the executables for these programs to your PATH variable. Don’t screw this up. It isn’t hard to undo screw-ups, but it will freak you out. Before you continue please read the excellent summary of shell startup scripts as they pertain to OSX here:

http://hayne.net/MacDev/Notes/unixFAQ.html#shellStartup

Assuming that you are new to the command line, and did not have a .bash_profile or .profile file already, the Anaconda install would have created .profile and added it’s executables to your path. From your home directory type:

nano .profile

Navigate to the end of the file and type:

export PATH=/Users/your-user-name/infernal/binaries:/Users/you-user-name/pplacer:${PATH}

Don’t be the guy or gal who types your-user-name. Replace with your actual user name. Hit ctrl-o to write out the file, and ctrl-x to exit nano. Re-source .profile by typing:

source .profile

Confirm that you can execute the following programs by navigating to your home directory and executing each of the following commands:

cmalign esl-alimerge pplacer guppy

You should get an error message that is clearly from the program, not a bash error like “command not found”.

Now you need to install the final dependency, Seqmagick. Confirm the most current stable release by going to Github, then download it:

curl -O https://github.com/fhcrc/seqmagick/archive/0.6.1.tar.gz tar -xzvf 0.6.1 cd 0.6.1 python setup.py install

Check the installation by typing:

seqmagick mogrify

You should get a sensible error that is clearly seqmagick yelling at you.

Okay, now you are ready to download paprica and do some analysis! Download the latest stable version of paprica (don’t just blindly download, please check Github for the latest stable release):

curl -O https://github.com/bowmanjeffs/paprica/archive/paprica_v0.23.tar.gz tar -xzvf https://github.com/bowmanjeffs/paprica/archive/paprica_v0.23.tar.gz mv paprica-paprica_v0.23 paprica

Now you need to make paprica_run.sh executable

cd paprica chmod a+x paprica_run.sh

At this point you should be ready to rock. Take a deep breath and type:

./paprica_run.sh test

You should see a lot of output flash by on the screen, and you should find that the files test.pathways.csv, test.edge_data.csv, test.sample_data.txt, and test.sum_pathways.txt in your directory. These are the primary output files from paprica. The other files of interest are the Guppy output files test.combined_16S.tax.clean.align.phyloxml and test.combined_16S.tax.clean.align.jplace. Check out the Guppy documentation for the many things you can do with jplace files. The phyloxml file is an edge fattened tree of the query placements on the reference tree. It can be viewed using Archaeopteryx or another phyloxml capable tree viewer.

To run your own analysis, say on amazing_sample.fasta, simply type:

./paprica_run.sh amazing_sample

Please, please, please, read the manual (included in the paprica download) for further details, such as how to greatly decrease the run time on large fasta files, and how to sub-sample your input fasta. Remember that the fasta file you input should contain only reads you are reasonably sure come from bacteria (an archaeal version is a long term goal), and they should be properly QC’d (i.e. low quality ends and adapters and barcodes and such trimmed away).

Drones in a Cold Climate - Eos

Featured News - Tue, 01/19/2016 - 12:00
As climate change reshapes the Earth's polar regions, scientists turn to drone-mounted cameras to measure sea ice. Lamont-Doherty's Frank Nitsche and colleagues explain the challenges of flying drones near Antarctica. It's tougher than it looks.

In Isolation, Community

Sampling the Barren Sea - Tue, 01/19/2016 - 10:38

By Frankie Pavia

I was talking to a colleague on board today while we were subsampling sediment cores we had taken from the last station. The cores were especially interesting – the entire surface was covered in manganese nodules, some the size of baseballs. Our conversation was interrupted by a mysterious occurrence. In one of the subcores we’d taken, there were manganese nodules sitting at 15 cm and 18 cm deep in the sediment. Conventional wisdom and that infamous beacon of knowledge, scientific consensus, stated that the nodules stayed on top of the sediment and were never buried after formation. There were also bright streaks of white carbonate nearby polluting the otherwise pristine red clay that occupied the rest of the core.

manganese

Mysterious manganese nodules in a core.

We had been talking about what it would be like to be back on land after a long cruise like this. My colleague has been to sea a few times before, and I was curious as to what she thought would be the most different to us upon returning to dry land. She explained that for her, the biggest change was interacting with strangers. There are only 64 people aboard the boat, and by now I can match a name to every face. I may not speak to them regularly, but I may have seen how they take their coffee, or what kind of cake they prefer in the afternoon, or exchanged a casual “moin” (hello) in the hallway. I haven’t seen a new face in almost four weeks.

I anticipated that being at sea might be lonely. I knew I would miss my friends and family. It has hit especially hard the past two Sundays when my hometown NFL team, the Seahawks, have played playoff games. I usually watch Seahawks games with my best friends in New York and fire texts back and forth to my friends I grew up with the entire time. Those are the times I am most in contact with the people I love. Sitting alone in my cabin aboard the ship, frantically updating Twitter, trying to follow the happenings and score of the game, feels especially isolating.

In a way, being a scientist is an isolating endeavor, no matter what. A friend of mine who writes for a hip-hop website is easy for any music lover to connect with. I talk to him every time a new mix tape drops, debating which tracks are the most fire. Another friend works for a soccer analytics company; he tracks the most popular sport in the world. I talk to him every time I’m watching an entertaining game or have a question about a soccer article I’ve read. But not many of my friends have burning questions about isotope geochemistry. The rare conversations we have had about protactinium have tended to be short and one-sided. I love talking about my research. I love learning about other peoples’ research. On land, I have limited opportunity to have these conversations.

On the ship, these conversations are nonstop. Oceanography is what the scientists on board all have in common – how could we not constantly talk about it? I might not know what someone’s favorite color is, or what town they grew up in. But I could probably give a pretty solid explanation of the questions they’re trying to answer with their research. I’ve detailed the systematics of protactinium and thorium isotopes countless times to other scientists on board and gotten genuinely interested responses, rather than blank stares. I began to understand what my colleague meant about interacting with strangers being the most difficult thing about returning to land. Returning to land will mean returning to the real world. There, my research and much of my identity will get suppressed until I can find my way back to the company of fellow scientists.

But as I had that realization, I was immediately distracted. The manganese nodules had made their first appearance within the deep sediment where they didn’t belong. Reality on land could wait. My colleague and I began to volley back and forth ideas about how they could have been emplaced so deep, and what experiments we could design to test our hypotheses. This is my beautiful reality at sea.

California's Crop-Sustaining Kern River at Lowest in 2,000 Years - Bakersfield Californian

Featured News - Fri, 01/15/2016 - 12:00
Although there have been longer droughts, the 2015 water year represents the driest in the last 2,015 years, and the 2012–2015 drought represents the driest four-year period, according to a study involving tree ring research from Lamont's Ed Cook.

January El Niño Update: It’s Got a Lot Going On - NOAA

Featured News - Thu, 01/14/2016 - 10:41
Lamont's Adam Sobel discusses connections between the Madden-Julian Oscillation (MJO) and this year's El Nino.

Ocean Observatory Will Study Underwater Volcanoes - Business Insider

Featured News - Wed, 01/13/2016 - 14:02
The system of sensors will allow scientists to study how the Earth continually sculpts itself. Lamont's Maya Tolstoy, who studies underwater volcanoes, describes its value to science.

Monster Tsunami May Have Created Madagascar's Giant Sand Dunes - Live Science

Featured News - Wed, 01/13/2016 - 12:00
Sometime in the past 8,000 years, a meteor may have hit the Indian Ocean, triggering a monster tsunami that struck Africa, new research from Lamont's Dallas Abbott suggests.

The 40,000-Mile Volcano - New York Times

Featured News - Tue, 01/12/2016 - 09:20
Scientists have inaugurated a major new effort to study the volcanic structures at mid-ocean ridges. Off the West Coast, they have wired up a highly active ridge with hundreds of sensors and cameras. Lamont's Maya Tolstoy discusses the project and what scientists are learning about seafloor volcanism.

Aerosols, Land-Use Changes and the Weakening Monsoon - The Hindu

Featured News - Sat, 01/09/2016 - 12:00
The South Asian Monsoon has been weakening since the 1950s with an increased incidence of extreme rainfall events. The Hindu talks with Lamont's Deepti Singh about the causes.

How El Niño Is Impacting California’s Wine Industry - Vox Media

Featured News - Wed, 01/06/2016 - 12:00
Lamont's Kyle Frischkorn and Logan Brenner write about the impact of El Niño's rains on California's vintages.

North Korea Blast: Seismic Signals for Hydrogen Should Be Bigger - CNBC

Featured News - Wed, 01/06/2016 - 12:00
The North Korean government announced a successful test of a hydrogen bomb, but some seismologists question the size of the blast. CNBC speaks with Lamont's Paul Richards and Won-Young Kim, director of the Lamont-Doherty Cooperative Seismographic Network.

How Scientists Know the North Korea Blast Probably Wasn't an H-Bomb - Bloomberg

Featured News - Wed, 01/06/2016 - 12:00
An actual hydrogen bomb has a seismic signature similar to an atomic weapon's, but its explosive yield is much larger, says Lamont-Doherty seismologist Won-Young Kim, director of the Lamont-Doherty Cooperative Seismographic Network.

Arctic Outbreak Barreling Toward U.S. May Be Storm Frank's Revenge - Mashable

Featured News - Mon, 01/04/2016 - 12:00
For most of the U.S., the weather through mid-January will be the polar opposite of what it was in December. To what do we owe this reversal of atmospheric fortune? Andrew Freedman talks to Lamont's Richard Seager and other scientists.

Earthquake Shakes Parts of New Jersey & New York - Journal News

Featured News - Sat, 01/02/2016 - 12:00
A 2.1 earthquake struck northern New Jersey early Saturday. Lamont-Doherty's Leonardo Seeber spoke with the Journal News about it.

Above-Freezing North Pole Caps Year of Arctic Extremes - VOA

Featured News - Thu, 12/31/2015 - 12:00
While the average global temperature has risen 1 degree Celsius since pre-industrial times, the Arctic is up 3 degrees. "The Arctic is warming much faster than we thought it would. And it's warming even faster than most of our models predict it will,” said Lamont's Bob Newton.

All I Wanted for Christmas Was for These Pumps to Work

Sampling the Barren Sea - Wed, 12/30/2015 - 08:58
The cruise track and sampling stations for the FS Sonne.

The cruise track and sampling stations for the FS Sonne.

By Frankie Pavia

We’ve just completed our first full station and are remarkably pleased with the results. We collected 8 seawater samples to measure helium isotopes; 20 to measure thorium and protactinium isotopes; 7 in-situ pump filters to measure particulate thorium and protactinium isotopes; 6 manganese oxides cartridges that were attached to the pumps to measure actinium and radium isotopes; and 1 box core of the ocean floor to measure sedimentary thorium and protactinium isotopes. I was going to make this paragraph into the Twelve Days of Christmas song, but 7 pumps-a-pumping doesn’t really roll off the tongue that well.

pump

A pump destined for the deep.

What all this means is that the first station was a smashing success for us. The only thing that didn’t quite go as planned was the nine-meter-long gravity corer coming up empty. We suspect it may have been due to the corer not being able to penetrate the hard carbonate layer we saw–about 15 centimeters thick in our box core. Nonetheless, we are delighted.

We were especially pleased that our in-situ pumps worked. We arrived on the cruise with the knowledge that the pumps would be there, but figured that somebody would be an expert on how to program them, maintain them and operate them. The pumps are essentially motors hung on a line deep in the water, drawing thousands of liters water through a filter, catching the ocean’s suspended particles.

After a week of poring over the manual, we were finally ready to deploy the pumps. It would take them 2.5 hours to descend to 3600 meters water depth, 6 hours of pumping, and 2.5 hours for the deepest pump to return. A convenient time to have them pump is overnight. Sleep is hard to come by while on station, so six hours of pumps pumping away at depth is a great excuse to scuttle off to bed.

We were pretty nervous as to whether they would actually work. We had invested a lot of time and energy getting them up and running. What a bummer it’d be if they spent six hours in the deep ocean not doing anything because I had accidentally programmed them to pump at the wrong time, or something. Our test run the previous day had been a bit spotty, too. The flow rate of the pumps had been something like 3 times lower than it should have been.

We woke up at 4 a.m. the next day to wait for the pumps to arrive back on deck, driven by caffeine and nervous energy. Christmas had been two days previous. On Christmas Eve the crew put on a terrific party in the hangar, and the pumps had been decorated with big red ribbons. We were about to find out whether the pumps were a present we actually wanted, or if they were one of those fancy battery-powered toys you get with a list of parts that has three missing and ends up never working.

All the pumps have names. We were able to name the four new pumps after ourselves, while the other four pumps already names. Claudia, Bernhard, Sebastian, Frankie, Laura, Frauke, Jimmy and Hulda. They all seemed to have a little personality too – especially the old ones, Laura, Frauke, Jimmy, and Hulda. Parts of Laura were backwards, Hulda’s screws refused to come loose, Jimmy’s pump head had missing pieces.

Claudia was the first to arrive at the surface. Immediately upon getting her out of the water, we put a shower cap over the filter holder to protect the filter from contamination by atmospheric aerosols and any dust floating around the hangar. We pumped the remaining water from the bottom through the filter, removed the filter holder and brought it to the lab. We carefully unscrewed the top, opened it up, and…

The filter was covered in particles! One by one, the pumps came up with filters that were coated by an even distribution of particles. Everything worked perfectly. Even Laura, Hulda, and Jimmy, though they were stubborn above water, did everything they were supposed to do once they were submerged.

We plan to measure protactinium and thorium isotopes on the particles to learn about the kinetics of particle movement in the ocean – sinking rates, absorption coefficients for trace metals, and export fluxes. Particles are the vectors that move elements out of the surface ocean, so studying their characteristics will be crucial for understanding how things like carbon and iron are pumped and exported to the deep.

Functional pumps meant that it was a happy Christmas for us. The next full station starts this afternoon. We’ll spend 42 hours sitting in one place, measuring dissolved, particulate, and sediment samples. Yesterday we had to change all the batteries on the pumps. Each pump requires 24 D batteries per deployment, and uses them all. So for every cast of 8 pumps, we use 192 D batteries. We’ll send the pumps out tonight and retrieve them at 4 a.m. again tomorrow morning.

We’re hoping these pumps are gifts that keep on giving.

Arsenic Contaminates India's Drinking Water - Scientific American

Featured News - Tue, 12/29/2015 - 09:37
In this video, Lamont-Doherty's Lex van Geen discusses how agriculture and irrigation are changing underground water flows, rerouting them through contaminated ground.

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