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Almost Home, with Another 7 Million Years of Climate History

When Oceans Leak - Fri, 03/25/2016 - 17:54
 Tim Fulton/IODP

Expedition 361’s scientists aboard the JOIDES Resolution, near the end of a successful two-month expedition. Photo: Tim Fulton/IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

We reached our last site yesterday morning, off Cape Town, South Africa, and the first core was on deck at 11:15 a.m. It was pretty stiff at the bottom, and its microfossils indicated it was more than 250,000 years at 1 meter. We decided to start again, and ended up with 6 meters in the first core of the B hole, with further indications of a very low sediment accumulation rate of approximately 1.5 cm per thousand years. The next few cores gave us troubles with shattered liners and low recovery, so Ian and I went back to the data from the alternative sites to consider moving. Luckily we decided not to, because things really started looking up.

We just completed the first hole with 300 meters of sediment and a base age of more than 7 million years, and with a quite pleasing accumulation rate below the very top part. We still don’t have quite enough information to evaluate the situation in the upper 1 million years, but it seems very clear that the rest of the site will be excellent. The sediment composition is very similar from top to bottom and very rich in carbonate (so called nannofossil ooze). The gamma ray (measures radioactivity and thus is a sensitive measure of clay) and color measurements give a very nice signal and are varying in concert with each other. The weather has gotten nicer since the beginning of the first hole, and we are hoping the conditions hold and that the sea conditions were the reason for the troubles at the beginning of our first hole. Meanwhile, we have just enough time to complete the triple coring of this site back to 7 million, with maybe enough time for logging of the final hole.

 Jens Gruetzner, Alfred-Wegener-Institut for Polar and Marine Research)

Crew members retrieve the beacon. Photo: Jens Gruetzner, Alfred-Wegener-Institut for Polar and Marine Research

So, the good fortune continues. Each site on this cruise has provided real prize material, and the team members are very eager to get started on the work back at home. We have been burning the midnight oil (or midday, depending on your shift), meeting about the various plans for post-cruise science. There remain a couple of conflicts to resolve, but overall it looks like there will be plenty of great science for each participant, and plenty of opportunities to develop career-long collaborations.

It has been a great privilege to be part of this, and it really makes you realize how powerful these huge efforts, that require the cooperation of so many countries and their scientists, are. It is a very different way of doing science, and not always convenient for the individual, but overall the benefits are huge.

Meanwhile, this is my last post for this cruise. We are less than a week from arriving at our dock in Cape Town, and there is no question that we are all quite eager to get there. The JOIDES Resolution is amazing and the (multiple) staffs of the ship company, catering service, and IODP are truly remarkable. They are friendly, professional and very eager to help us to get the best we can out of this amazing scientific discovery process.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

 Tim Fulton/IODP

The crew and scientists of Expedition 361. Photo: Tim Fulton/IODP

Antarctic wind-driven bacterial dispersal paper published

Chasing Microbes in Antarctica - Thu, 03/24/2016 - 12:53
Frost flowers over young sea ice in the central Arctic Ocean. Photo Mattias Wietz.

Frost flowers over young sea ice in the central Arctic Ocean. Photo Mattias Wietz.

I’m happy to report that one of the appendices in my dissertation was just published in the journal Polar Biology.  The paper, titled Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region, was a long time in coming.  I conceived of the idea back in 2010 when it looked like my dissertation would focus on the microbial ecology of frost flowers; delicate, highly saline, and microbially enriched structures found on the surface of newly formed sea ice.  Because marine bacteria are concentrated in frost flowers we wondered whether they might serve as source points for microbial dispersal.  This isn’t as far-fetched as it might seem; bacteria are injected into the atmosphere through a variety of physical processes, from wind lofting to bubble-bursting, and frost flowers have been implicated as the source of wind deposited sea salts in glaciers far from the coast.

At the time we’d been struggling to reliably sample frost flowers at our field site near Barrow, Alaska.  Frost flowers form readily there throughout the winter, but extremely difficult sea ice conditions make it hard to access the formation sites.  We knew that there were more accessible formation sites in the coastal Antarctic, so we initiated a one year pilot project to sample frost flowers from McMurdo Sound.  By comparing the bacterial communities in frost flowers, seawater, sea ice, terrestrial snow, and glaciers, we hoped to show that frost flowers were a plausible source of marine bacteria and marine genetic material to the terrestrial environment.  Because the coastal Antarctic contains many relic marine environments, such as the lakes of the Dry Valleys, the wind-driven transport of bacteria from frost flowers and other marine sources could be important for continued connectivity between relic and extant marine environments.

Frost flowers are readily accessible in McMurdo Sound throughout the winter, however, this does not mean that one can simply head out and sample them.  While the ice conditions are far more permissible than at Barrow, Alaska, the bureaucracy is also far more formidable.  The can-do attitude of our Inupiat guides in Barrow (who perceive every far-out field plan as a personal challenge) was replaced with the inevitable can’t-do attitude at McMurdo (this was 2011, under the Raytheon Antarctic Support Contract, and does not reflect on the current Lockheed Antarctic Support Contract, not to suggest that this attitude doesn’t persist).  Arriving in late August we were initially informed that our plan was much to risky without helicopter support, and that nothing could be done until mid-October when the helicopters began flying (we were scheduled to depart late October).  Pushing for a field plan that relied on ground transport ensnared us in various catch-22’s, such as (paraphrased from an actual conversation):

ASC representative: You can’t take a tracked vehicle to the ice edge, they’re too slow.

Me: Can we take a snowmobile to the ice edge?  That would be faster.  We do long mid-winter trips in the Arctic and it works out fine.

ASC representative: No, because you have to wear a helmet, and the helmets give you frostbite.  So you can only use a snowmobile when it’s warm out.

Ultimately we did access the ice edge by vehicle several times before the helicopters started flying, but the samples reported in this publication all came from a furious two week period in late October.  What we found really surprised us.

Sampling frost flowers is as easy as scraping them from the ice surface with a clean shovel into a sterile plastic bin.

Sampling frost flowers on a warm day in September, 2011, in McMurdo Sound.

Pull very short ice cores from young sea ice after sampling frost flowers. You can see one of the short cores in the lower right of the image.

Sampling some of the frost flowers used in this study over much thinner ice north of Ross Island in October, 2011.

 Shelly Carpenter.

Sampling “blue ice” on Taylor Glacier a few days earlier.  Comparing various terrestrial ice environments with the marine samples gave us some interesting insights on how bacteria are dispersed by strong winter winds in the coastal Antarctic.

There is ample evidence for the wind-driven transport of bacteria in this region but, contrary to our hypothesis, most of that material is coming from the terrestrial environment.  The major transportees were a freshwater cyanobacterium from the genus Pseudanabaena and a set of sulfur-oxidizing Gammaproteobacteria (GSO).  The cyanobacterium was pretty easy to understand; it forms mats in a number of freshwater lakes and meltponds in the region.  In the winter these freeze, and since snow cover is low, ice and microbial mats are ablated by strong winter winds.  Little pieces of mat are efficiently scattered all over, including onto the sea ice surface.


Easily dispersed: desiccated microbial mat in Lake Chad, 2005
(photo by A. Chiuchiolo), taken from

The GSO threw us for more of a loop; the most parsimonious explanation for their occurrence in frost flowers is that they came from hydrothermal features on nearby Mt. Erebus.  We did some nice analysis with wind vectors in the region and while you don’t get a lot of wind (integrated over time) to move material from Mt. Erebus to our sample sites, you do get some occasional very strong storms.

Wind velocity and magnitude for the study region in October, 2011. Taken from Bowman and Deming, 2016.

Wind velocity and magnitude for the study region in October, 2011. Taken from Bowman and Deming, 2016.

What all this means is that, consistent with other recent findings, there is high regional dispersal of microbes around the coastal Antarctic.  While I’m sure there are some endemic microbes occupying particularly unique niches, in general I expect microbes found in one part of the coastal Antarctic to be present in a similar environment in a different part of the coastal Antarctica.  There are however, quite a few ways to interpret this.  Bacteria and Archaea can evolve very fast, so the genome of a clonal population of (for example) wind deposited Pseudanabaena newly colonizing a melt pond can diverge pretty fast from the genome of the parent population.  This has a couple of implications.  First it means that the coastal Antarctic, with all it’s complex topography yet high degree of microbial connectivity, is an excellent place to explore the dynamics of microbial adaptation and evolution, particularly if we can put constraints on the colonization timeline for a given site (non trivial).  Second, it raises some questions about the propriety of commercially relevant microbes obtained from the continent.  The commercialization of the continent is probably inevitable (I hope it is not), perhaps the potential ubiquity of Antarctic microbes will provide some defense against the monopolization of useful strains, enzyme, and genes.

Tracking Earthquakes in the New York Area - Fox News

Featured News - Thu, 03/24/2016 - 12:00
The devastation caused by earthquakes is evident all across the world, but could something like this happen in our area? Fox news talks with Jim Gaherty.

Heavy Breathing Plants Producing Less Carbon than Feared - Geographical

Featured News - Wed, 03/23/2016 - 12:00
When plants respire, they contribute a massive carbon flux to the atmosphere so their response to higher temperatures is a major concern for scientists. A new study from Lamont's Kevin Griffin finds plants might not respond to warming as thought.

Wine-Lovers Raise a Glass to Climate Change, but There May Be a Hangover - Guardian

Featured News - Mon, 03/21/2016 - 13:00
Higher temperatures in France are producing exceptional vintages, but the run will come to an end if global warming continues at the current rate, a new study from Lamont's Ben Cook suggests.

France's Top Wines Face Climate Tipping Point - AFP

Featured News - Mon, 03/21/2016 - 12:00
Climate change has pushed French wines into uncharted territory, and could force producers to relocate or abandon the grapes that helped to make their vineyards famous, according to a study from Lamont's Ben Cook.

Warming Pushes Wine Harvests Earlier – Not Necessarily for the Better - The Conversation

Featured News - Mon, 03/21/2016 - 12:00
"Our analysis showed that wine harvests are happening earlier, which has historically been a harbinger of high-quality wines. But we also found that changing local weather conditions could make it harder to determine when to expect high-quality wines, and that higher temperatures could force wine growers to use different grape varieties," writes Lamont's Ben Cook.

Carbon Emissions Top Even Those of 56 Million Years Ago - Christian Science Monitor

Featured News - Mon, 03/21/2016 - 12:00
Carbon emissions hit a dramatic high nearly 10 million years after the demise of the dinosaurs some 66 million years ago. But emissions now far surpass that. "What we're doing today is much more extreme than what happened in Earth's history," says Lamont's Bärbel Hönisch.

Will Our Trees Survive the Warming Temps? - Public News Service

Featured News - Mon, 03/21/2016 - 09:37
A crew of scientists led by Lamont's Park Williams has been making its way through the Ozark Mountains, dodging snakes and poison ivy to study tree rings, to see how they're reacting to climate change.

Finding Microfossils Off Southern Africa

When Oceans Leak - Sat, 03/19/2016 - 19:13
 Dick Norris and Jason Coenen. Illustration by Deborah Tangunan

Expedition 361 micropaleontologists with their nannofossil specialties (not quite to scale …): Top, left to right: Margit Simon, Thiago Pereira dos Santos, Luna Brentegani and Deborah Tangunan. Bottom: Dick Norris and Jason Coenen. Illustration by Deborah Tangunan

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

Limpopo was awesome! We ended up with close to 4 million years of sediment from our latest coring site, off Mozambique near the Limpopo River. The accumulation rate for the last 2 million years is close to 10 cm per thousand years, so there is potential for highly resolved records in that interval. The accumulation rate between about 2 million and 4 million years is much lower, probably about a quarter, but that is also good news because we only had permission to go 250 meters, and if there had been more sediment we wouldn’t have covered nearly as much time.

The foraminifera are spectacular – translucent, glassy and “very pretty” throughout the whole sedimentary section. We do have a gap or two, as hard as we tried to avoid it, but we have overlap among holes for most of the site, and a continuous record back to close to 2 million years.

During coring at the Zambezi site earlier this week, the micropaleontologists had less to do since there were only two biostratigraphic datums (one foraminifera and one nannofossil), so nannofossil specialist Debs Tangunan made some cute art (above) with each of the biostratigraphers upon a fossil type of his or her specialty. Debs and Luna are the nannofossil specialists; Dick and Thiago are the planktonic (shallow floating) foraminifera specialists; Margit is the benthic (from the bottom) foraminifera specialist; and Jason is the diatom specialist. Jason’s pouting because most of our sites have not been good for diatom biostratigraphy, except the Agulhas Plateau. He has been a great sport though and has been helping with sample preparation and picking benthic foraminifera for a preliminary stable isotope record to help refine the age models for our sampling party.

The Agulhas Current. Image courtesy of Arnold Gordon.

The Agulhas Current. Image courtesy of Arnold Gordon.

We finished up at Limpopo this afternoon and now we are heading south to our final site, which is in the Cape Basin, and only eight hours from the harbor at Cape Town, South Africa. The catering staff put on a fantastic show for the 5-7 p.m. meal – it was sushi!  And what a beautiful layout, with butter carved into the shapes of fish and various melons and other food. It was delicious and amazing!

During the transit to the Cape Basin, which will take a little over four days, we will have a busy time finishing the cores from Limpopo and the Mozambique Channel. We had to put ~1/2 of a hole’s worth of cores to the side to get the shallow sites completed, and we will finish up those cores as we transit to the CAPE site. We must have all the data collected and reports finished before we arrive at CAPE because we are going to have to devote our full attention to the CAPE site in order to get the report finished on that site before we get to port.

CAPE is located right were the eddies that constitute the “leakage” from the Agulhas Current enters the Cape Basin. So this site is going to be very important for tying together the story of how the Agulhas Current system is connected to global ocean circulation. The water depth of CAPE (as well as the other three of our deeper sites from this cruise: Natal Valley, Agulhas Plateau and Mozambique Channel) is in North Atlantic Deep Water (NADW). So we should be able to obtain some great co-registered records of how the shallow and deep ocean circulation are changing through time, as well as how the productivity and temperature and salinity have varied and how these are related in time to southern African climates.

//">Cardiff Half Marathon</a> to raise money for a charity by running the distance aboard ship. Photo: Tim Fulton/IODP

Stephen Barker (left) and Ian Hall prepare to participate in the March 26 Cardiff Half Marathon. They’ll be raising money for a South African education charity by running the 13.1 miles in laps around the ship’s helideck. Photo: Tim Fulton/IODP

Another exciting thing that is going to happen while we are at CAPE on March 26, is that Co-Chief Scientist Ian Hall and Stratigraphic Correlator Steve Barker, both from Cardiff University, are going to be running a half marathon around the deck of the JOIDES Resolution at the same time the Cardiff Half Marathon is underway in the UK. Steve is a former Lamont postdoc and an adjunct associate research scientist at Lamont.

Their goal is to raise funds for a charity that supports children in South Africa. The small South African charity, located in the Western Cape, is called the Goedgedacht Trust, and it promotes education to help poor rural African children escape grinding poverty.  We are also planning to provide some of the Trust’s children with a tour of the ship during our visit in Cape Town. Ian and Steve will appreciate any support you (or your colleagues) can give!  Donations can be made online. I’m planning to contribute, and I hope you will too.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

China's Forest Conservation Program Shows Proof of Success - Christian Science Monitor

Featured News - Sat, 03/19/2016 - 12:00
"When it comes down to climate and carbon sequestration, these are global problems," says Lamont's Kevin Griffin.

California City Worries About Expansion and Future Water Supply - The Tribune

Featured News - Sat, 03/19/2016 - 12:00
Worried about how climate change will affect rainfall in the coming decades, some San Luis Obispo residents are calling on the city to stop allowing developers to build new homes — at least until the city recalculates its future water supply.

How Israel Survived the Levant's Worst Drought in 900 Years - JNS

Featured News - Fri, 03/18/2016 - 15:53
A combination of water from rainfall, recycling of wastewater, desalination of seawater, and a large-scare water conservation campaign helped Israel get through what research from Lamont's Ben Cook shows is the region's worst drought in more than 900 years.

So, Was That Climate Change? - CNN

Featured News - Thu, 03/17/2016 - 17:17
Scientists are increasingly able to attribute aspects of extreme weather to the overall change in the climate, as John Sutter discusses with Lamont's Park Williams.

A Surprise from the Zambezi River

When Oceans Leak - Wed, 03/16/2016 - 20:05
//">JOIDES Resolution</a>. Photo: Tim Fulton/IODP

Alexis Armstrong and Beth Novak of the International Ocean Discovery Program (IODP) prepare a core for laser engraving aboard the JOIDES Resolution. Photo: Tim Fulton/IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

We have finished coring the Zambezi site and are on our way to the Limpopo site. Both are just off shore from major rivers that flow through Mozambique and should provide a record of the terrestrial climate variability in southeastern Africa through time, but we discovered a surprise. Based on short cores from nearby, as well as seismic surveys, we were expecting that the sediment accumulation would be 10 cm per thousand years. We were wrong by almost 10 times. The accumulation rate is approximately 1 meter per thousand years. Luckily, one of the scientists has been studying records from short cores, and the correlations to them is very clear even though the accumulation rates are so much greater, and we have two biostratigraphic datums that are further consistent.

So with our 200 meters of core we were only able to get back to 200,000 years instead of the 2 million years we anticipated. This is happy news on one hand, as this will allow some extraordinarily highly resolved records of climate variability back to approximately 120,000 years, and maybe (with small gaps) back to 200,000 years. But it is also disappointing from the view of the goal to get a long record of climate variability in the Zambezi catchment. It allows different kinds of questions to be pursued, and they are also very valuable. We feared encountering a bunch of sand, and that did not happen, so all in all this was a successful site, and we are still absorbing the change of approach that would be required to get the most out of it.

Expedition 361's coring sites. APT is the Agulhas Plateau. NV is the Natal Valley.

Expedition 361’s coring sites.

We should get to the Limpopo site at about midnight ship time (Cape Town time) tonight, and expect the first core on deck early Thursday morning. It seems highly unlikely that our estimate of sediment accumulation will be much different, but we are eager to find out! The location of our site is on the outside of a terrace feature in the indentation feature on the African margin (both the Zambezi and Limpopo enter the Indian Ocean in distinctive indentations on the eastern margin of southern Africa). Based on the seismic cross sections, the deposit is what is called a “plastered drift,” it is a body of sediment that is built up by bottom currents flowing southward along the margin. So even though the site is in the Limpopo area, its location relative to the currents is such that we may expect to get a similar record here as well. We will need to make some careful comparisons using the many existing short cores to establish how to best apply and interpret our methods.

Meanwhile, things are very busy on the ship. We were not able to complete the measurements and description of the final hole from the highly successful first Mozambique site before arriving here, and we are still working on the Zambezi cores as we approach the Limpopo site. We hope to keep up the pace so we will be finished with both soon. We expect the coring at Limpopo to take approximately two full days. Then we have about four days transit to our final site, CAPE, off the tip of South Africa. We want to have all three site reports completed before we arrive at CAPE since we will have no scrap of extra time after that!

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

Some Trees Could Help Fight Climate Change - Science

Featured News - Wed, 03/16/2016 - 12:00
Compared with trees suddenly exposed to hot temperatures, acclimated trees may release far less CO2 at night, a new study suggests. Science talks with Lamont's Kevin Griffin.

Helping the Earth Store Carbon - Fusion

Featured News - Mon, 03/14/2016 - 09:11
Lamont's Peter Kelemen discusses ways of using mantle rocks as natural carbon capture and storage solutions.

Mozambique Core Brings Up 7 Million Years of Climate History

When Oceans Leak - Fri, 03/11/2016 - 17:00
 Tim Fulton/IODP

Scientists crowd around the stratigraphic correlators’ screens as new details come in. Co-chief scientists Sidney Hemming and Ian Hall are on the right, joined by Luna Brentegani, Christopher Charles and Stephen Barker. Photo: Tim Fulton/IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

We just completed coring at our northernmost Mozambique site. The sea is still. The weather is hot and muggy, but so still. This is how sediment coring should be. The stratigraphic correlators think they are having a dream. We have no gaps, beyond the absolute minimum from the coring process, and the variability in the physical properties makes correlating among the holes dead easy.  And the variability looks like a fantastic, cyclic climate signal that is continuous back to 7 million years ago!

We are heading to the Zambezi site now. For our two river sites – offshore from the Zambezi and Limpopo Rivers – our big goal is making the most direct connection possible between what happened on land and in the oceans over the past ~2 million years. We’re only expecting about 2 million years because the accumulation rates are higher, but the nice thing about that is that we can get much more detail about the variability.

 Tim Fulton/IODP

The drilling crew works with equipment aboard the JOIDES Resolution. Photo: Tim Fulton/IODP

Among our science party, we have multiple tools to probe how the rainfall may have changed through time. We have organic biomarkers as well as several measures of terrigenous (land-derived) sediment sources, weathering intensity and fluxes. The Zambezi catchment is located at the very southern part of the annual shift in the Intertropical Convergence Zone (the so-called thermal equator), so there is a strong gradient to drier climate to the south.  And that is one of the reasons having both the Zambezi and Limpopo is so exciting to think about. The “great grey-green greasy“ Limpopo catchment is much drier than the Zambezi.

We are going to be so busy. We have finished the coring and yet more than half the cores are waiting to be processed for the various observations and measurements we have been making. We will get to the Zambezi site in less than two days, and the water depth is much shallower there, meaning the cores are going to come up every 20 minutes or so rather than every 45 minutes, as at the northern site. And then we only have about one more day to get to the Limpopo where the same rate of coring is expected.  So we are going to be buried in cores by the time we finish at Limpopo, and we’ll have about four days to finalize the data collection and reports before arriving at our final site, CAPE, off the tip of South Africa. More about CAPE later.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

Links Between Climate Change & Extreme Weather Increasingly Clear & Present - Washington Post

Featured News - Fri, 03/11/2016 - 12:00
Our science has reached the point where we can look for the human influence on climate in single weather events, and sometimes find it, writes Lamont's Adam Sobel.

Building the paprica database

Chasing Microbes in Antarctica - Fri, 03/11/2016 - 11:04

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment.

Build the paprica database provides maximum flexibility with paprica but involves more moving parts and resources than conducting analysis with paprica against the provided database.  Basic instructions for using the script are provided in the manual, this tutorial is intended to provide an even more detailed step-by-step guide.


While a laptop running Linux, VirtualBox, or OSX is perfectly adequate for analysis with paprica, you’ll need something a little beefier for building the database (unless you’re really patient).  A high performance cluster is overkill, I build the provided database on a basic 12 core Linux workstation with 32 Gb RAM (< $5k).  Something in this ballpark should work fine, of course more cores will get the job done faster (but keep an eye on memory useage).

Once you’ve got the hardware requirements sorted out you need to download the dependencies.  I recommend first following all the instructions for the script, then installing RAxML and pathway-tools.  The rest of this tutorial assumes you’ve done just that, including running the test file.

Install remaining dependencies

In addition to all the dependencies required by you need pathway-tools and RAxML.  These are very mainstream programs, but that doesn’t necessarily mean installation is easy.  In particular pathway-tools requires that you request a license (free for academic users).  This takes about 24 hours after which you’ll receive a link to download the installer.  Regardless of whether you’re sitting at the workstation or accessing via SSH a GUI will pop up and guide you through the installation.  In general you can accept the defaults, however, the GUI will ask you where pathway-tools short create to directory ptools-local.  This is where the program will create the pathway-genome databases that describe (among other things) the metabolic pathways in each genome.  By the time you are done creating the database this directory will be > 100 Gb, so pick a location with plenty of space!  This may not be your home directory (the default location).  For example on my system my home directory is housed on a small SSD.  To keep the home directory from becoming bloated I opted to locate ptools-local on a separate SATA drive.

You will receive a number of download options from the pathway-tools development team.  I recommend that you conduct only the basic installation of pathway-tools, and do not download and install additional PGDBs.  Nothing wrong with installing these additional, well-curated PGDBs other than increased space and time, but they become ponderous.  You can always add them later if you want to become a metabolic modeling rock star.

To be continued…



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