Posts tagged GOS

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Back To Sampling In The Black Sea and Rough Rough Weather

September 9th 2010

Hello everyone!  I know it has been a long time since the last post from Sorcerer II.  Let me take the time to explain………… early August we sailed to Greece.  As I have mentioned in the past we have permits with each country to collect samples, these permits have certain time windows and other country specific stipulations.  Once stipulation on the Greek permit was that for each Greek sample collected we must have a Greek collaborator onboard Sorcerer II. 

One of the biggest problems when scheduling sampling on a sailboat is the weather……….and trust me weather is going to be a topic on many upcoming blogs.  So there we were, certain dates we could legally sample during, dealing with the most intense weather systems in Sorcerer II history, and scheduling local observers to be onboard (the month of August is much like the states, lots of people taking vacation at the end of the summer, so getting someone on the boat at the right time was a big challenge).  We decided to make our way up the Aegean Sea through the Sea of Marmara and into the Black Sea.  With most weather systems blowing from the north this would put us in a great position to do an intense month of sampling back down to Crete.  The problem was actually getting up the Aegean Sea; we had many days where we had to stay on anchor in sheltered bays due to 30-40 knot head winds.

Map of the upcoming sampling transect

During the month of scheduling and positioning of Sorcerer II we took the time to let crew take personal time off the boat, do some PR about the expedition with major Greek news media and Dr. Venter was able to give lectures in Athens, Greece and Sofia, Bulgaria.  I can’t lie; we also sailed around some of the most beautiful places I have ever seen, more on this on my “tourist” blog coming up about Greece.

Satellite Imagery of Aegean and Black Sea

On Sept 7th Sorcerer II left the dock from Nessebar Bulgaria on what was planned to be a 2 week sampling transect from the Black Sea, through the Bosphorus and Sea of Marmara into the Aegean Sea down to Crete.  We collected 6 samples from 3 Black Sea sites, including the deep anoxic zone.

CTD Profile of the Anoxic Black Sea

Nessebar Bulgaria

Virtual Comparative Metagenomics

We have created an open virtualization format (OVF)  package of JCVI’s Metagenomics Reports (METAREP)– a high performance comparative metagenomics analysis tool. The software runs on a web server, retrieves data from two different database systems and uses R for statistical analysis. The new OVF package bundles all these 3rd party tools and is configured to run out of the box in a virtual machine.

Screenshot of the virtual box appliance import wizard. The wizard allows you to specify the CPU and memory usage of the virtual machine on which METAREP will run on.

To run a virtual version of METAREP on your machine, follow these steps

  1. download the METAREP OVF package from our ftp site [download] .
  2. unzipp the OVF package
  3. download and install Oracle’s Virtual Box, a OVF compatible virtualization software [download]
  4. Start Virtual Box
  5. Click File/Import Appliance and select the OVF file.
  6. Adjust RAM/CPU usage using the Appliance Import Wizard (see image)
  7. Start VM
  8. Double-Click on the METAREP firefox link on the VM desktop
  9. Log into METAREP with username=admin and password=admin

This virtual machine appliance is the first step in developing a fully cloud-enabled analysis platform where users can easily launch the application wherever is most convenient: on their personal desktop or in the cloud where they can scale-out the appliance to suite their needs.

Future virtual machine images will be certified to run on other virtualization software platforms. Stay tuned.

If you like to learn more about METAREP and talk to the developers,  join us  at  Lucene Revolution Conference in Boston (October 7-8  2010). We will present a lightning talk about METAREP  the first day of the conference 5pm  (see agenda).





METAREP Source Code

Italy- Sites and Sailing

Saturday July 31st

When I last wrote we had finished our 10 day  sampling window in Italian waters. On Wednesday July 21st we arrived in Rome the same day Dr. Venter, Heather Kowalski, and Darwin the super boat dog had flown in from the states.  We spent 3 days in Rome, most of the time was spent doing media events, restocking the boat with supplies and trying to see as much as Rome as possible in our spare time.  On the night of July 23rd we set sail to make our way down the coast of Italy, tonight we will do the overnight sail to Greece.  I wanted to post some pictures of some of the beautiful places we have seen as we sailed in Italy.

Darwin In His Favorite Resting Position

Saint Peter's Basilica, Vatican City

Laocoonte, Vatican City

Ponza Island

Coliseum, Rome

Water Spout

Vulcano Island

View Of Vulcano Island

Porto Santo Stefano At Night

Crater Of The Volcano in Vulcano Island

Capri Island

Vatican City, Rome

10 Days of Italian Sampling Coming to a Close

Tuesday July 20th

On July 16th we finished our Straits of Messina sampling and headed into the Ionian and Adriatic Seas.  We sailed overnight and collected our Ionian Sea sample,  we continued  northeast and  on July 18th we collected our Adriatic Sea sample.  After we collected the Adriatic Sea sample we turned around and headed back to the Straits of Messina to resample the south entrance on July 19th.  We proceeded through the straits directly to Ponza Island where we anchored tonight July 20th.

CTD Profile Of South Side Of Messina Straits Taken on July 16th

CTD Profile Of South Side Of Messina Straits Taken on July 16th

CTD Profile Of South Side Of Messina Straits Taken on July 19th

We have never really resampled a site in the same exact location a few days later, the profiles above are from the same GPS coordinates and the same time of day 3 days apart.  The fluorescence, Oxygen, and salinity look very similar but there are some slight differences in temperature down the water column.  These two samples could be very interesting to compare once they have been sequenced.

Since we entered Italian waters on July11th we have collected 24 samples from 11 different sample sites.  It was a very busy 10 day but a very successful!  We collected samples in all the different bodies of water  and unique environments as we had planned.  One of the reasons we were so successful was due to weather………we had calm winds and seas the entire time which made sample collection very easy, and made overnight passages possible (we only anchored 3 nights in 12 days).  Below are some pictures of the seas we had during different legs of this trip, sometimes it felt like we were on a lake it was so calm!  Tomorrow we sail the 50 miles to pick up Dr. Venter and do some Italian media events.

Ionian Sea Sunrise

Sunrise in the Ligurian Sea

Sunset in the Tyrrhenian Sea

Straits of Messina Transect

Friday July 16th

Today we woke up early and left our anchorage at Vulcano Island and headed to the Straits of Messina 20 miles away.  The plan was to collect a sample at the north entrance, anchor for 5 hours to process the sample.  Once the sample was completed then head to the middle of the straits collect another sample, anchor again process that sample, and pick up another sample on the south side of the straits and keep sailing towards the Adriatic Sea.

Map of the Straits of Messina (Red X )

Satellite Image of Straits of Messina

The Strait of Messina is 20 miles (32 km) long and from 2 to 10 miles (3.2-16 km) wide, separating the Italian peninsula from Sicily and connecting the Ionian and Tyrrhenian seas. The massive amounts of water being funneled into a relatively small space creates strong currents and whirlpools.  Since this is the area where two big bodies of water meet, we wanted to make sure we collected samples along a north/south transect.

John helping collect the sample in the middle of the Straits of Messina

Swordfish Boat

Swordfish Boat

As we collected our samples we saw a lot of these swordfish fishing boats.  The boat is actually driven by one of the guys on the top of the mast, also up there are a couple spotters.  They are looking for swordfish that sleep during the day near the surface.  Once they find one they can slowly approach it and a harpoonist launches a harpoon from the extremely long bowsprit!

Another Swordfish Fishing Boat

Sunset as we left the straits and headed into the Ionian Sea

Advance Access JCVI Metagenomics Reports Application Note

A significant JCVI informatics development is JCVI Metagenomics Reports, an open source Web 2.0 application designed to help scientists analyze and compare annotated metagenomics data sets. Users can download the application to upload and analyze their own metagenomics datasets.

METAREP has just been published in Bioinformatics (08/26/2010) as an open access article. The publication is currently accessible under the Bioinformatics Advance Access model. The PDF version can be downloaded at

Supplementary information includes the METAREP data model and an overview about its search performance accessible at

One of METAREP’s  key features that distinguishes it from other metagenomics tools is that it utilizes a high-performance scalable search engine that allows users to analyze and compare extremely large metagenomics datasets, e.g. datasets produced by the Human Microbiome Project.

If you like to learn more about METAREP and talk to the developers,  join us  at  Human Microbiome Research Conference in St. Louis in Missouri (August 31 – September 2, 2010). We will present METAREP  the first day of the conference at 10:35am (see agenda).

Contact Us:

We would like to hear from you. If you have questions or feedback or if you wish to contribute to the METAREP open source project please send an email to





METAREP Source Code

Naples Harbor Sampling

Thursday July 15th

After getting some sleep at anchorage in Ischia island we sailed for a few hours to the main harbor in Naples.  Over the years the Sorcerer II Expedition has collected samples in major ports around the world (Sydney, Halifax, Boston,  Panama, Cape Town, just to name a few).  Naples harbor is not only a big industrial harbor but also a research site that has been monitored by Italian scientist for may year.

Naples Harbor With The USS Dwight D. Eisenhower Aircraft Carrier Anchored

Water Profile from Naples Harbor

As you would imagine from such a busy port the water was not clear blue like open ocean!  We could only filter 200 liters from the surface (normally we can easily do 400 liters) and 75 from the Chlorophyll max (we can normally do 200 liters).

After we collected our Naples sample we sailed overnight to the Southern Tyrrhenian Sea and collected samples from above a  thermal vent off of Lipari Island.  Once we had the samples collected we sailed to Vulcano Island to anchor for the night and prepare for the 3 samples we would collect the next day as part of our Straits of Messina transect.

Vulcano Island

Italian Sampling Continues-Unique Animal in Italian Waters!

Wednesday July 14th

Monday July 12th we woke up early and left the anchorage in Capraia Island.  We arrived at Ischia island at 5:00 a.m. on Wednesday the 14th.  In those  48 hours we collected 6 samples.  Two samples were collected in the Northern Tyrrhenian Sea, two samples were collected over a seamount in the Tyrrhenian Sea and two other samples were collected at a long term research station in the Tyrrhenian Sea.  It was a pretty intense 48 hours of sampling.

Night Sampling

Deepest Profile Ever Collected on Sorcerer II

I have been on Sorcerer II since  2003 and I have seen a lot of things at sea, whales breaching, sharks swimming around, dolphins, flying rays, I even saw a shark eating a dead whale near Nantucket (nobody believes me, but I swear it happened!), but what we saw the other day 30 miles offshore wins the prize for the strangest thing I have ever seen at sea!  John spotted something in the water so we changed course to see what it was!

The Cow-Pig Ahead!

Cow-Pig Close Up

Another View Of The Cow-Pig

As we passed this giant dead animal, there were two things it could be, a cow or a pig!  People disagreed so that night we decided to just call it a cow-pig.  As pictures were downloaded of the famous cow-pig we all took a look at the tail and feet, we all agree now it is a big bloated pig, but feel free to let us know your thoughts!  Either way it was strange to see this so far from land!

Mediterranean Sampling Season Starts

Sunday July 11th 2010

On Thursday July 8th Sorcerer II set sail from Valencia Spain to start the Mediterranean season.  Permits vary from country to country, Italy gave us 10 days to collect our samples, so we had to time our departure from Spain to fit our 10 day sampling window in Italy.  As we sailed to Italy we collected a sample in French waters from a long term research site important to French scientist.

Italian Sample Sites

Our planned route is to sail along the north coast of Italy into  the Ligurian Sea and Gulf of Genoa, head down the  the west coast, through the Strait of Messina around the boot and into the Adriatic Sea.  The sample sites in Italy include, shallow thermal vents, seamounts, long term research sites and sites where large bodies of water collide and mix.Today we collected our first Italian sample between the Ligurian Sea and Gulf of Genoa then headed to anchor in a bay off  Capraia Island for the night.

CTD Cast Profile In Northern Italian Waters

Karolina and Jeremy Collecting Samples

It has been only 3 nights at sea, but being anchored or docked is always better for a good nights sleep!  Tonight we hope to watch the World Cup Final, which should be fun except we are not in Spain any longer!!  Then it is an early rise to set sail down the west coast of Italy.

The Sorcerer II Sampling Process

July 6th

 In the blog about the media event I posted a few days back I put a link to the JCVI media page.  On this page you can learn about our research goals, funders and past expeditions (more links on the right side of the page).  Before we set out for this sampling season I wanted to explain how we actually collect our samples on Sorcerer II.

One question I get asked a lot is “How do you pick your sample sites?”  Well a team at the JCVI that includes Bob Friedman, Sarah Dyste, Andy Allen and Chris Dupont work with collaborators from the countries we will be collecting samples.  The collaborators give us the coordinates of research sites that they are interested in.  In most cases these sites have years of data associated with them.  It is our goal to pair metagenomic data with the ongoing in country research to establish a fruitful scientific collaboration.

Once all the proper permits are in place,  Karolina, Captain Charlie and myself chart out the best sample route that will allow us to collect the most unique samples and avoid rough weather and seas.  Once we arrive at a sample site the first thing we do is lower the CTD (which stands for Conductivity, Temperature and Depth).  As the name implies it measures temperature, depth, salinity as well as fluorescence, pH, and dissolved oxygen.  As the CTD is lowered it gives real time data that is graphed on a computer in the cockpit.



Jeremy and Karolina lowering the CTD off the back of Sorcerer II

CTD graph as the CTD moves down the water column

Once a profile is complete we decide where to collect our sample, from Sorcerer II we can collect water from 120 meters (393 feet).  Most of the time the sample is collected in the  chlorophyll max, but not always, we also are interested in low oxygen zones, salinity gradients and thermoclines.  Once an area in the water column is chosen, 200 liters of water is pumped up from depth.  At the same time 400 liters is collected from the surface waters, both depths are pre-filtered  through a 200um nytex net.  

The water is pumped via a small compressed air driven pump through a series of decreasing filters (3.0um, 0.8um and 0.1um).  Based on the CTD profile of the water column 200 liters of the filtered seawater  from the surface or deep sample is recollected and run through a Millipore tangential flow filtration device (TFF) with a 50 Kda cartridge.  The TFF removes excess seawater but retains all the viruses in the sample. 

Graphic on how the samples are processed (note the net should be 200um)

Filter racks and TFF system

0.8um filters. Left is from the surface sample. Right is from the deep sample

The filters are removed from the rack, stored in buffers and placed in the -80 degree Celsius freezer we have in the engine room.  2 liters of the viral concentrate in 10% glycerol  are stored at -20 degrees Celsius.  Other subsamples for nutrient analysis, flow cytometry, pigment, and microscopy work are stored in the appropriate buffer/temperature.   The entire sampling process takes about 7-9 hours.  The samples are shipped back to the laboratories in La Jolla and Rockville on dry ice when we get to a major port.

We also have a fluorescent microscope which displays on the HD television.

Microscope on Sorcerer II