Tuesday, 22 July 2014

OSD Consortium

OSD is the world’s first simultaneous megasequencing campaign.  Having taken place for the first time on the June 2012 solstice, four pilot events took place before the Main OSD Event in June 2014.  Plans are taking shape to continue to 2015 and ideally beyond.  OSD is completely dependent on the collaborative participation of marine researchers around the globe taking samples from sites of special scientific interest.  Many of the initial sites joined because they are dedicated to long-term marine research and as such, are taking part in the Genomic Observatories (GOs) Network.  As OSD events progressed additional sites have joined, often with the added benefit of bringing more diverse locations for sampling into the OSD fold.

Due to the success of this ‘crowd-sourced’ project, a large network of sites and researchers has now come together (more than 180 for June 2014).  At the 16th meeting of the Genomic Standards Consortium at the University of Oxford, the community agreed to formalize into the Ocean Sampling Day Consortium.  

Combined, the OSD Co-ordination Team and the Network of sites, contribute to the infrastructure and expertise that allows co-ordinated OSD events to take place.

As part of the Consortium, participants are formally part of the OSD Network of sites, get access to training activities under Micro B3, and samples are prioritized for all types of data generation (as funds and resources allow) and bioarchiving.

In return, participants agree to provide samples according to OSD protocols (see the OSD Handbook) and work under the umbrella of the OSD Data Policy which requires open sharing of data, appropriate legal framework for sampling and agreement to publish within the consortium.

Here we describe how to join and participate in the OSD Consortium.  

Joining the OSD Consortium

1.  The first step is to fill in an expression of interest.

2.  You will then be contacted and asked to join in a Skype telecon to assess your interest and decide on steps forward.

3. All sites must be registered in the OSD Sites Registry to formally be recognized as part of the OSD Consortium.  To do so requires a named co-ordinator for each site and contribution of basic descriptors of the site.

4.  Once formally registered, sites can take part in OSD sampling events according to the OSD Handbook.

5. Contributed samples must conform to ABS, MTA and Data Policy requirements.

6. All sites will be invited to take part in publication on the whole OSD data set and to join the OSD Analysis Working Group.


Expression of interest:

Registering a Site in the OSD SItes Registry:

OSD Handbook:

Thursday, 10 July 2014

Ocean Sampling Day in the Antarctic – this time around, we were early!

This year we managed to get out on the 17th of June. As the weather forecast is very unreliable and another weather window was not in sight, we decided to take the opportunity and get the samples early. When we left base in our RIB it was still snowing and it took us quite a while to push through the pancake ice but we finally got to Site 1 (see Figure 1). The fast ice edge was just where we wanted to sample which was good as it was slightly too windy and we would have drifted quite a lot. However, we found a little bay and were able to throw an anchor onto the ice to stop us from drifting. During the 2 ½ hours we were out there, the weather cleared up and it turned into a quite beautiful day. Despite the sun not rising currently, it got quite light and the wind calmed down.

Click here to a little video we have put together.

Figure 1: At Rothera we have 3 Sites we commonly visit for CTDs. Site 1 is 500m deep and allows us a full CTD profile. Site 2 is closer to base and only 200m deep but less likely to be covered by ice in the winter. Site 3 is just off the wharf and only about 100m deep. This side is only visited if the ice is too thick to get any further.

Like last year we filtered 2l for each of the 4 replicates through Sterivex filters. They were put into the -80°C freezer for preservation until the ship picks them up in March 2015.
For us in Antarctica, the 21st of June is a very special day being the winter solstice. It marks the day with the least daylight. At Rothera this means that we still get a couple of hours of daylight (without seeing the sun), but others spend their days in complete darkness. As Christmas is not quite as big as a deal down here as it is at home, midwinter is celebrated much more. At the beginning of winter we all pick names out of a hat (like secret santa) and had to make a present for the person we drew. Lots of amazing things were made like hammocks, clocks, cake stands, models of sledges, a real size sledge, a Banjo case and more. We got together in the morning at around 11am (just when it started getting light) for breakfast. We met up again at 2pm all dressed up nicely, ate canapés and exchanged presents. At 4pm we started the epic journey of an 8-course dinner. We had an interval at 7.30 just before the main course for our mid-winter broadcast. This is the only time of the year the BBC World Services transmits in a way that we can pick it up. They put together a 30min show for all British bases with the songs of our choices, maybe a celebrity we asked for and most importantly messages from our loved ones at home – quite special and emotional.
Sabrina Heiser, Rothera Marine Assistant

Crew: Mairi Fenton (Marine Assistant for the Dutch collaboration), Petra Mildeova (Meteorologist)

Rothera is a British Antarctic Survey research station, located on Adelaide Island on the Antarctic Peninsula at 67° South.

The whole team with the presents (Photo: Chris Walton)

Thursday, 5 June 2014

Protocols and Documents for OSD Main Event Participation - June 21st, 2014 Saturday

Dear All,

Below is a list of links to all relevant protocols and documents required for participation at the OSD Main Event on June 21st, 2014, Saturday.

MTA & Data Policy documents need to be signed, scanned and sent to osd-contact<at>microb3<dot>eu by June 13th, 2014. Hard copies to be shipped together with your samples by July 23rd, 2014 to Bremen, Germany.

You can purchase any of the below:

3. OSD Sampling Protocol for Prokaryotes

8. OSD Sites Registry

9. Micro B3 OSD Data Policy

10. Micro B3 OSD Smithsonian Institute Material Transfer Agreement

11. CIESM Charter
To be circulated by Dr. Michele Barbier, CIESM.

As always, massive thanks for all your efforts.

OSD is what you make of it..

Best wishes,
The OSD Core Team

Friday, 2 May 2014

Final Micro B3 / OSD Data Policy

Final Micro B3 / OSD Data Policy

Authored by the OSD Data Policy Working Group with the OSD Consortium

OSD Data Policy Working Group

Dawn Field, Oxford University, OSD, WP2 Leader
Mesude Bicak, Oxford University, OSD Co-ordinator/Bioinformatician
Anna Klindworth, MPI Bremen, OSD Co-ordinator
Frank Oliver Glöckner, Jacobs University Bremen & MPI Bremen, Micro B3 Coordinator
Arianna Broggiato, BIOGOV, ABS (WP8)
Arul Scaria, BIOGOV, Data Policy (WP8)
Tom Dedeurwaerdere Univ Louvain WP8 Leader
Alban Ramette, AWI, Biostatistics (WP5 & WP6)
Linda-Amaral Zettler, Woods Hole, MicroB3 Scientific Advisory Role (ICOMM MIRADA LTER)
Petra ten Hoopen, EBI, Metadata & Standards (WP2 & WP4)
Michelle Barbier, CIESM, Med Co-ordinator (WP2, 4, 8 & 9)
Neil Davies, UC Berkeley, GOs Network, WAML, Pacific Region
Jack Gilbert, Argonne National Labs, EMP
Katie Barker, Smithsonian Institution, GGI Bio-Archiving

Status to date

This data policy covers the collection, dissemination, analysis and publication of OSD data.  It was developed over the past years of OSD pilot events. Within Micro B3, WP8 is responsible for the Micro B3 data policy.  The OSD policy is based on this policy and consultation with the OSD Consortium.  It was finalized at the Micro B3 General Assembly (GA) April 2014. It remains the responsibility of the OSD Data Policy working group to make sure the policy is fit for purpose and all are aware of it when submitting and using data of the OSD Consortium.  If you would like to join the group please contact osd-contact@microb3.eu.We welcome input from all OSD participants on shaping of the OSD data policy. Please send comments to osd-contact@microb3.eu.


The OSD Data Policy was created by drawing on existing policies (See Biosharing: http://biosharing.org/policies) and current best practice in genomics and the needs of Micro B3 and the OSD community.  It was developed and will be maintained according to the “12 steps to a data policy” outlined in Field et al (2009) Science:

12 Step Path to a Data Policy:

Tenets of Ocean Sampling Day (The policy applies to all in the OSD Consortium. It is a mandatory part of taking part in OSD)

The OSD data set is generated by the members of the OSD Consortium - to be part of the Consortium you must be formally registered and substantively contribute to the collaboration.

The OSD dataset will be a reference data set and should be as widely accessible and used to support downstream research as possible.

As OSD is one event (a one-off event) it should be easier to get all contributors (their official sites) to release the data publicly.

All OSD data must be standards compliant - must include metadata - this includes compliance with the Micro B3 standard, which includes the GSC’s MIxS standard.

All OSD genomic data must be tightly linked to environmental data - contextual information is a top priority.

Sequence data without deposition of accompanying metadata (minimum of lat, long, time, depth, temp, salinity according to OSD Handbook) will not be released after the June solstice 2014 event.  The OSD Consortium will work towards release of all data.

The OSD data policy covers the pilot events, the main OSD event and any subsequent events.

Data must be submitted to the public repositories (e.g. INSDC).  Micro B3 will make sure 2012-2015 data sets are submitted to the ENA/MG-Portal.
All data will be processed/stored in the Micro B3 infrastructure as it is built and the full data set will eventually be available through this infrastructure. Data can flow in many analysis pipelines/databases - we welcome its wider use

All samples must be collected legally (with appropriate permits) and individual collectors are responsible for making sure of this.  Specifically ABS/MTA/DTA agreements will be in place as required (bioarchiving at GGI requires OSD MTA, proof of relevant ABS and metadata)

The OSD Consortium

This data policy applies to everyone in the OSD Consortium (to date this means everyone who has constructively contributed to OSD sampling events).

Release of the data and metadata

At the 2013 EEB meeting of the Micro B3 project we agree on the importance of the OSD data set as a whole (the sum of participating sites) and the desire to support open sharing of the data.  The EEB agreed to work towards: ”immediate release of all OSD data as soon as sequenced and quality checked to the public”.  In this, sense “public” means beyond Micro B3 and OSD participants to the public at large.  To protect the rights of the consortium to publish the first global analysis of the data, the data will be released under Ft Lauderdale principles.  This is routinely used in large sequencing projects and promotes the use of the data by the wider community while safeguarding the scientific contributions of the data generators.  For example, a complete Neanderthal genome was released to the public prior to publication in 2013 under these principle  (see: http://www.eva.mpg.de/neandertal/index.html).

This statement will accompany all access to OSD sequence data.

Use of the sequence data

All data will be made freely available. However, we ask users to observe the Ft. Lauderdale principles, which entitles the data producers to make the first presentation and publish the first genome-wide analysis of the data.  The data can be used freely for studies of individual genes or other individual features of these sequences.

Collaborative Data Analysis

We hope that the OSD reference data set will be helpful in a variety of ways and we encourage those interested in analysis of the data to declare their interests and formally join the OSD Data Analysis working group.  Together, we are working towards “OSD reports” that will be generated following each event.  Ideally, each report will provide a high level overview of the event and, if multiple events are available, comparison and contextualization with past data.  Predictions about future events may also be included.  It is our vision that this type of transparent collaboration where interested parties declare how they would like to contribute to the data analysis,  will help maximize the efforts of the community and build the strongest possible biological interpretation of the data.


We expect the authorship of the global analysis of the OSD data set to belong to the OSD Consortium.  Authorship will be defined on a case-by-case basis for more specialist publications.

Evolution of this Policy

According to the “12 steps for policy development” process, this policy may evolve according to best practice.  As agreed at the May 2013 EEB meeting of Micro B3, changes to the policy will be done in consultation with the community.  Specifically, policy issues will be taken forward through the OSD Data Policy Working group who is responsible for building consensus on any issues or changes. Final authority for any changes and for upholding the policy will rest with the leadership of Micro B3

Signed by

Site ID:                         ………………………………………………….............            
Site Name:                   ………………………………………………….............
Institution:                   ………………………………………………….............
Country:                      ………………………………………………….............
Site Coordinator:        ………………………………………………….............
Signature:                    ....................................................................................

Date:                             …………………………………………………………..

Thursday, 6 February 2014

Ocean Sampling Day‐ Winter solstice 2013‐12‐20 at Faxaflói, Iceland – Matis

Sampling was performed for the fourth time in Faxaflói, a bay in Southwest-Iceland between the peninsulas of Reykjanes and Snæfellsnes. A small boat was used to go to the OSD sampling station (N64°12.457’ W22°00.878’) in a ruff sea and a strong wind (wind speed 16-20 m/sec) and air temperature of 0.9°C. Despite of heavy rolling and unstable conditions on board the small boat, we manage to collect three replicate samples from the sampling station from a depth of 0.2 meter using acid cleaned bucket. The sampling was at 14:25 o´clock on the day before winter solstice 2013‐12‐20.The water samples (1 L) were filtrated almost instantly on site through four 0.22 μm Sterivex filters (Millipore). Filters were sealed and immediately frozen at ‐80°C. 

Additional site information:
Air temperature: 0.9°C 
Water temperature surface: 2.1 ̊C
Salinity 3,5
Wind speed 16-20 m/sec

All the best from Viggó and Eyjó

View to the shore from the sampling site

Two crew members (Eyjó and Viggó) working on deck

Google map snapshot of the OSD sampling site

Viggó Thór Marteinsson, Eyjólfur Reynisson and Kristinn Guðmundsson 

Wednesday, 29 January 2014

OSD Pilot Event on December 19th 2013 at Venice Acqua Alta Platform (OSD63)

OSD Site 63 Venice Acqua Alta Platform (North Western Adriatic Sea)

The sampling site is the Acqua Alta oceanographic platform, a site for long term ecological research (LTER) operated by the Institute of Marine Science of the National Research Council of Italy. The tower, built in 1970, is located at about 10 nautical miles off the city of Venice, at the water depth of 16 meters. Acqua Alta currently serves as a multi-disciplinary station for a wide variety of marine researches, and is equipped with a meteo-oceanographic station (providing measurements of temperature, wind, humidity, solar radiation, rain, waves and tides), sensors for the main hydrological parameters, and underwater webcams. Instruments can be controlled remotely, and real time data are available. It is part of the LTER network and decadal time series are available at ISMAR-CNR about the trophic state of the area, the ecology and biodiversity of plankton, and the biogeochemistry.

Due to the adverse meteorological conditions forecasted for the 20th, the OSD sampling was carried out on the 19th December. We left from the pier in front of the Institute around 9:00 onboard the boat Litus. Water sampling was performed at 2:00 pm. The sea conditions were calm and the weather was sunny. In addition to collecting samples to be filtered onto Sterivex for bacterial diversity analyses, we performed CTD casts for measuring the main physical-chemical variables and collected water samples for phytoplankton/zooplankton abundance, and the determination of total suspended matter and chlorophyll.

The OSD team of the ISMAR–CNR in Venice before departure. From left to right: Mauro Bastianini, Gian Marco Luna, Grazia Marina Quero and Lucia Bongiorni.

The OSD sampling site 63: the oceanographic tower Acqua Alta operated by the ISMAR-CNR.

A view on the Northern Adriatic Sea from the upper floors of the tower.

Live phytoplankton cells observed in the water samples collected during the pilot event.

We are looking forward to the OSD sampling day in 2014!

Gian Marco Luna (OSD Site 63 coordinator), Grazia Marina Quero, Lucia Bongiorni, Mauro Bastianini – Institute of Marine Science, National Research Council of Italy, Venice (Italy)