WHO’S WHO IN THE ZOO – MEG SCHWAMB

In this week’s edition of Who’s who in the Zoo Meg Schwamb tells us more about the Planet Four: Terrains project.

– Helen

 


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Project: Planet Four: Terrains

Researcher: Meg Schwamb, Assistant Scientist

Location: Gemini Observatory, Hilo, Hawaii

 

What are your main research interests?

I study how planets and their building blocks form and evolve, applying ground-based surveys to probe our Solar System’s small body reservoirs and citizen science to mine large datasets for Solar System science.

 

Who else is in your project team? What are their roles?

Candy Hansen (PSI) is the PI of the project, K-Michael Aye (LASP) & Anya Portyankina (LASP) are also members of the science team.

 

Tell us more about the data used in your project

The images reviewed on Planet Four: Terrains come from the Context Camera (CTX) aboard Mars Reconnaissance Orbiter (MRO). The Context Camera takes black and white wide view images (~30 km x ~60 km with ~6 m/pixel resolution) of the Martian surface that we cut into smaller chunks reviewed on the site.

 

How do Zooniverse volunteers contribute to your research? 

We ask volunteers to review the CTX subimages of the South Polar region of Mars and identify whether they see specific features: (1) araneiforms (including features with a central pit and radiating channels known as ‘spiders’) carved by carbon dioxide jets; (2) erosional depressions, troughs, mesas, ridges, and quasi-circular pits characteristic of the South Polar Residual Cap (SPRC) which we collectively refer to as ‘Swiss cheese terrain’, and (3) craters.

 

What have been the biggest challenges in setting up your project?

Figuring out the format and contents of the classification exports.

 

What discoveries, and other outputs, has your project led to so far?

Our first paper was accepted last year to a journal. Planet Four: Terrains has identified new regions of carbon dioxide jet activity including areas with jet carved channels (spiders/araneiforms) on geologic units previously thought to be resistant to the process (locations the spiders/araneiforms weren’t expected to be). More details here (http://blog.planetfour.org/2017/08/29/planet-four-terrains-first-science-paper-accepted-for-publication/).

 

Once you’ve finished collecting data, what research questions do you hope to be able to answer?

What is the distribution of aranaeiforms (spiders) over the South Polar regions? Why do we find araneiforms (spiders) in specific locations outside of the South Polar Layered Deposits?

 

What’s in store for your project in the future?

Expanding to a larger search area and exploring areas further from the South Pole of Mars to see how far North spiders may exist.

 

What are your favourite other citizen research projects and why?

I’m currently involved in several Zooniverse projects, so I think they are all my favorites: Planet Four, Planet Four: Ridges, and Comet Hunters.

 

What guidance would you give to other researchers considering creating a citizen research project?

Be cognizant that combining the multiple volunteer classifications together is likely very different from what you’ve done in the past for data analysis. Also, treat your project volunteers’ as your collaborators.

 

And finally, when not at work, where are we most likely to find you?

Baking and watching soccer (hoping the Chicago Fire make the playoffs).

 

For more information, check out the Planet Four Blog Post.

 

 

 

 

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Who’s who in the Zoo – Martin Jones

In the third of our Who’s who in the Zoo series, meet Etch A Cell‘s Dr Martin Jones

– Helen

 


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Project: Etch A Cell

Researcher: Martin Jones, Deputy Head of Microscopy Prototyping

Location: Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK

 

What are your main research interests?

Imaging and image analysis.

 

Who else is in your project team? What are their roles?

Lucy Collinson (head of EM STP) leads the EM team, Chris Peddie (Principal Laboratory Research Scientist) acquired the data, Anne Weston (Senior Laboratory Research Scientist) performed the expert analysis.

 

Tell us more about the data used in your project

The images are from our “serial block face scanning electron microscope” and are of small groups of HeLa cells (a type of cancer cell). The electron microscope allows us to see objects down to a few billionths of a metre in size. Each cell is divided up into around 200-300 individual sections (like a loaf of sliced bread) so we can see the insides of the cell. To start with we hope to analyse around 50 cells, but as a core facility we have an endless supply of different types of data we’d like to analyse!

 

How do Zooniverse volunteers contribute to your research? 

The Zooniverse volunteers help us with our “segmentation” task – tracing a line over the nuclear envelope, which is a very important membrane inside the cell that separates the nucleus from the rest of the cell.

 

What have been the biggest challenges in setting up your project?

One of the key advantages of the citizen science approach is that we can have several different volunteers analyse each image, allowing us to combine the results to get a statistical understanding of the data. Combining the volunteers’ work in the most effective way possible turns out to be pretty tricky though! Especially since our data is stored as lots of individual lines, meaning a simple average doesn’t really work.

 

What discoveries, and other outputs, has your project led to so far?

The first thing we wanted to make sure was that the data we get is good enough, which thankfully it looks like it is! Even that was perhaps a bit unexpected to some people! We’ve found it has been popular as an education and outreach tool too, with reports of teachers using it in their classes to teach about cells. We’ve also shown it off at an event at the Natural History Museum in London and a CRUK event in Manchester and spoken about it at several conferences around the world. We’re writing up the first journal article about it right now in fact!

 

Once you’ve finished collecting data, what research questions do you hope to be able to answer?

While electron microscopy produces amazingly detailed images, there are very few studies where data has been fully quantified at large scale, since it’s such a labour-intensive process at the moment. By measuring the shapes of each object (nucleus, mitochondria etc.) in different types of cell we can perform robust quantitative comparisons that are not currently possible. This sort of knowledge will help us to understand many different diseases, like cancer, malaria and tuberculosis, as well as help us find effective treatments for those diseases.

 

What’s in store for your project in the future?

There’s a lot more to come from Etch a cell! We have plenty more data that we’d like to analyse in the same way – tracing outlines – but for some other objects inside a cell we think a different approach might be easier and more effective. We’re working on a few options, and hopefully future iterations will be easier for people to work with on mobile devices. In parallel, we’re also building an artificial intelligence system to use the results from Etch a cell to enable us to train computers to be as good at the task as humans.

 

What are your favourite other citizen research projects and why?

Bash The Bug was released at the same time as Etch a cell and is a really great project. EyeWire is another electron microscopy project that has been groundbreaking in the field of “connectomics” – trying to understand how the cells in brains are connected together. Cancer Research UK has produced several different projects with a great deal of success, it was our initial interaction with their team that brought citizen science to our attention in the first place.

 

What guidance would you give to other researchers considering creating a citizen research project?

Have a play around with the project builder, setting up a basic project is really easy!

 

And finally, when not at work, where are we most likely to find you?

I try to get outdoors as much as possible, whether that’s walking, running or cycling.

 

 

Penguins, Plastics, and Poo

This week’s guest blog post is from Dr Gemma Hall, who is leading a range of Zooniverse educational outreach initiatives in the UK. Read on to find out about the activities she led earlier this month during British Science Week.

– Helen

 


 

Penguins, Plastics, and Poo

Science Week, a week when we scientists gush about our favourite subject, attempt to explain to others what we do all day or just get plain messy with icky, sticky crowd-pleasing experiments. I think I successfully covered all these things during Science Week. And I have Zooniverse to thank for (most of) this.

I’m a STEM Ambassador (https://www.stem.org.uk), which means I do lots of science outreach. And I’m a huge Zooniverse fan. Whether it’s bashing bugs, elephant expeditioning or galaxy-gazing, I love that anyone with a computer/internet connection can help with real people-powered research, including children.

So, for Science Week, instead of just talking about what scientists do, I used Zooniverse to get primary school children being the scientists. Children like feeling important, so key to engaging them from the outset meant emphasising the importance of helping real researchers make the world a better place. Cue dramatic gasps and disbelieving looks all around the ICT Suite!

Children also like being able to relate to what they’re learning about. And so, I introduced them to the researchers they would be helping…

 

Penguins

 Scene: Children transfixed by a PowerPoint presentation showing a picture of Dr Tom Hart, of Penguin Watch, wrapped up against the harsh Antarctic elements, surrounded by penguins.

Tom is a Penguinologist, and I almost had to stop the teachers stampeding out of the ICT Suite in an effort to re-train so they too can get such a great job title. The children, meanwhile, were more captivated by the wondrous site of the hundreds of penguins.

I told the class that Tom’s laboratory is the Antarctic and he wears hefty, cold weather gear rather than a white lab coat. He studies penguins because they give us a really good indication of the effects humans have on the Antarctic. Tom needs to keep an eye on the penguins across many Antarctic sites, all day, every day of the year. However, I continued, Tom can’t live in the Antarctic all year because it’s too harsh and he’d miss his family. He has cameras taking hundreds of photos every day and now has so many that he needs help to analyse them.

And with that, the children keenly set about tagging penguins: Adelies, King, Gentoos, Chinstraps; adults, chicks and eggs. They were careful to observe the behaviour of the penguins and their habitats, which both gave indications of whether the penguins might be incubating eggs or caring for chicks. They imagined what working in the harsh Antarctic environment would be like and they were intrigued about what penguins get up to in the night!

The energy in the classroom could have powered the computers the children were using! And the concentration levels and tagging skills were higher than I’ve seen many adults apply (sorry, Adults!). Furthermore, they asked if they could continue helping to spot penguins at home, so huge was their passion to help.

If you want spot penguins too, go to: penguinwatch.org

 

Plastics

Scene: Children looking at a PowerPoint presentation picture of a beach, with Peter Kohler and Ellie McKay of The Plastic Tide flying their drone.

Plastics have been in the news lots recently and these children were very clued-up, so they needed little introduction to the plastic problem. Already sufficiently motivated to help clean up our planet, they were spurred on even more by hearing that the The Plastic Tide project is the official project of British Science Week and that it was featuring on Sky News and the BBC!

I explained that Peter and Ellie needed help to tag plastic or litter in beach pictures taken by drones. Tagging the pictures teaches a computer program to recognise plastic. The more pictures that are tagged, the better the program will become. Soon, computers will be able to find the plastics themselves, aiding the creation of a global inventory of marine plastic pollution.

The children set to the task with determination, but it soon became apparent that they were not all totally happy; some were frustrated that not all the images had plastics in. After a gentle reminder that we really shouldn’t be hoping to find plastics and that it’s better to have plastic-free beaches, they returned to the task, only to exclaim later that tagging plastics was making them angry. However, this time, they were annoyed that they had spotted so much plastic and litter. Among their finds we had shoes, old toys, many bottle tops, rope, plastic bags, scores of fragments and even an old, gnarled “danger” sign.

We calculated that in one class of 30 children, each child had tagged between 10 and 20 images, so all together they had helped tag an outstanding 300–600 images. With many other schools around the country also tagging plastics, no wonder the Science Week target to tag over 250 000 images was smashed within days. In fact, by the final day, The Plastic Tide had a record-breaking 1.5 million tags—6 times their original target! That equates to 290 000 a day or 800+ tags a minute!

I spoke to Peter at the end of Science Week and he was blown away by the energy and support:

“Science Week has been a huge boost to tagging. The more tags we get, the better the computer algorithm becomes at detecting plastic. Each tag could help find millions more of the same item and will help us clean up our beaches”.

Peter also confided that there are some very exciting announcements coming soon from The Plastic Tide, so keep an eye out for those, and KEEP TAGGING!

 

Poo

I bet you’re wondering where the “poo” in the title comes from? Well, that’s the icky sticky crowd-pleaser I was referring to at the start. Let’s just say that soggy Weetabix squeezed through nylon tights with a hole in the toe end is a really great way to demonstrate the intestine and how it results in… poo! And I’m also told that before you see a penguin colony in the Antarctic, you smell it first.

For a cleaner approach to science, use Zooniverse!

 

Get tagging!

Get your children tagging!

Help with REAL research and make the world a better place.

 


 

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Dr Gemma Hall is a Science & Technology Writer and STEM Ambassador. She loves explaining complex things simply, and enthusing people about the importance of science to their everyday lives. Gemma is working to develop Zooniverse in schools, enabling young people to perform real research so that they better understand what scientists do.

 

Email: gemmaSTEM@gmail.com

Twitter: @Gemma_STEM

Who’s who in the Zoo – Anabelle Cardoso

In the second of our series of ‘meet the researcher’ blog posts, meet PhD student Anabelle Cardoso, who leads the very popular elephant-spotting project, Elephant Expedition

– Helen

 


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Anabelle (fourth from left) and the on-the-ground research team at the research station in Gabon

 

Project: Elephant Expedition

Researcher: Anabelle Cardoso, PhD Candidate

Location: School of Geography and the Environment, University of Oxford, UK

 

What are your main research interests?

‘Elephant Expedition’ is part of my PhD research at the University of Oxford, which I started in 2015. Our research is about understanding how forest elephants affect the ecosystems they live in.

Forest elephants are extremely endangered, largely due to hunting for ivory. However, because they live in such mysterious and remote forests, we don’t know as much about them as we would like to. Learning more about these important and threatened animals is critical, as the better you understand an animals ecology the more effectively you can advocate for and plan its conservation.

In our study site in Gabon, and across Africa, valuable savanna habitat is being lost due to over-expanding forests as a result of human-induced global change. Normally, you wouldn’t think of growing forests as a threat, but savanna habitat is home to most of the remaining large mammals in Africa and performs many important ecosystem functions, including carbon storage, so loss of savannas is a global concern. Elephants are ecosystem engineers meaning that they have a disproportionately large impact on the ecosystems they live in. This gives then the unique potential to affect how much forest or savanna is in a landscape, so they can help protect savannas in the face of expanding forests. Most of the research on how elephants might do this has been done on bush elephants, which are a completely different species to the forest elephants of central Africa. Our research aims to remedy this by focusing on how forest elephants affect the forest and savanna balance of the landscape they live in.

In order to better understand forest elephants, we first need to know where they are, so we’ve set up a network of hidden camera traps to photograph them as they move through the forest. Our 40 camera traps are attached to trees and take a photo when triggered by motion or heat. They are super useful for monitoring dangerous and elusive animals like forest elephants because they function 24/7 and can give us a really good idea about where in the landscape the elephants are spending their time without us having to disturb the elephants by following them on foot. This is where the citizen scientists come in – because the camera traps are quite sensitive they don’t only capture images of elephants, but also gorillas, chimpanzees, buffalo, antelope, or even passing birds and bats. The citizen scientists help us to classify all the images into categories based on what’s in them. We can then convert these classifications into data about where the elephants are at what times of year, and link it with our other environmental measurements to draw conclusions. What the citizen scientists contribute is absolutely essential to the research, and forms the backbone of everything we do.

 

Who else is in your project team? What are their roles?

Yadvinder Malhi (Oxford), Imma Oliveras (Oxford), William Bond (University of Cape Town), and Kate Abenermethy (University of Stirling) supervise me; and Josue Edzang-Ndong (ANPN Gabon) and David Lehmann (ANPN Gabon, University of Stirling) and Kathryn Jeffery (ANPN Gabon, University of Stirling) help managed the project on the ground in Gabon. A special mention should be made to @melvinosky and @jwidness, our wonderful project moderators.

 

Tell us more about the data used in your project

We have 40 motion and heat sensitive cameras set up along rainforest edges in Gabon, they take photos of all passing animals (mostly elephants, but also a lot of gorillas, chimpanzees, buffalo, leopard, and red river hogs!). These are the images that the volunteers help to classify.

 

How do Zooniverse volunteers contribute to your research? 

In our project, volunteers are shown an image from one of our camera traps and they have to classify it according to what animal is in it. If the image contains a forest elephant, they also have to count how many elephants they see. The project is simple, so volunteers of all ages and skill levels can join, plus they can classify hundreds of images and therefore get lots of opportunities to spot cool animals.

The project’s feasibility relies on citizen scientists – from our network of hidden camera traps in the rainforest of Gabon we have nearly 2 million photographs we need to analyse and this would be impossible without the help of our dedicated volunteers. To date, there are 10,000 citizen scientists signed up on our website from all parts of the world, as long as you have an internet connection you can join the team.

Citizen science is wonderful because everybody benefits. As researchers we can process very large data sets (like our set of elephant photos) by harnessing the power of thousands of minds all working towards a common goal. This enables us to expand our research scope far beyond what would be possible as individuals – it’s the ultimate global collaboration. The citizen scientists benefit too. Volunteers are exposed to experiences that they might not otherwise have access to, for example in Elephant Expedition you essentially go on a virtual safari through the central African rainforest looking for forest elephants, gorillas, chimpanzees, leopards or mandrills (a type of monkey) – this just isn’t something most people will ever get the chance to do in real life. The project also has a vibrant online community of volunteers. One of the volunteers is a cancer sufferer and she says that participating in our project allows her to not be excluded from doing something just because she’s sick, it gives her a way to pass the time in hospital and makes her feel part of something meaningful.

Since we have so many camera traps and they are highly sensitive, we have many photographs – nearly 2 million! The photographs have a time and location stamp, so each time a volunteer classifies an image as having an elephant in it we know when and where that elephant was sighted. This information from the volunteers is synthesised and is what we’re using to build a time series of elephant habitat use across the landscape. Without the volunteers we would have no way of analysing the images, and therefore no data with which to answer our research questions. Citizen scientists play an integral role in the success of the project, the bottom line is that without them the project wouldn’t be able to work.

 

What have been the biggest challenges in setting up your project?

It isn’t really a challenge, more a learning journey. I think the amount of time it takes was a challenge, that you always have to be connected to answer questions and see to issues, and of course just learning how to manage such massive data sets has been a steep learning curve! It’s been great though, and I’ve been really humbled by the experience, because all of the volunteers on the project are so lovely and helpful it’s been amazing to be a part of.

 

What discoveries, and other outputs, has your project led to so far?

We haven’t started doing data analysis yet but we are very excited to see the results! We will be keeping all the volunteers updated on the project page as things continue.

 

What’s in store for your project in the future?

We have one more small run of final photos, and then we will begin the data analysis and writing up some research! It’s all very exciting and should be coming together in the next few months.

 

What are your favourite other citizen research projects and why?

Oh! I loved Snapshot Serengetti!

 

What guidance would you give to other researchers considering creating a citizen research project?

The potential for citizen science research is truly astounding. The world is a big place and the internet is able to connect us with one another. There are millions of potential volunteers across the globe who care as much about what you are researching as you do, and citizen science is an amazing way to connect with them. The best way to make a project effective is to find clever ways of linking volunteers and researchers according to the research interests of both. I think project effectiveness can also be measured by what both researchers and volunteers gain, for example did the research fulfil its scientific aims? Was the scope of the research enhanced by being able to use a global network of volunteers? Did the volunteers feel they gained some enjoyment and knowledge from the process of engaging with it? Would volunteers educate those around them about the research?

When designing a citizen science project, we found it most important to always remember that the people who volunteer to help you are smart and they care about what you’re researching. By including them in the project they become a part of the project, so always appropriately respect their time and skills. Our project depends on people sacrificing time out of their lives to help reach a research goal, so we always make sure we put in the time to communicate with volunteers, answer questions, and just generally engage personally with the people who make the project possible.

 

And finally, when not at work, where are we most likely to find you?

In Oxford, writing my thesis or destressing with some yoga, or maybe at home in Cape Town, South Africa, walking on the mountain or swimming in the sea. I also love to take road-trips across Southern Africa, there’s always something beautiful to see!

 

To learn more about Elephant Expedition, check out Annabelle’s Twitter account (@ellieexpedition) or Instagram Page (@elephantexpedition), or click here to go directly to the project.

The future of extreme weather forecasting, preparation and response

Below is a guest post from Robbie Parks, a PhD student from Imperial College London who is studying how global climate change is influencing human mortality. 

Read on to learn more about how crowd sourcing via platforms such as the Zooniverse can help us prepare for, and respond to, extreme weather.

– Helen

 


The future of extreme weather forecasting, preparation and response

Robbie Parks

 

The extreme weather around the globe during 2017 was a grim reminder of how truly devastating extreme weather can be. The citizens of Houston, New Orleans, Mumbai, Bangladesh, Nepal, Puerto Rico, the Dominican Republic, Florida and Sierra Leone joined the swelling ranks of victims from hurricanes and floods. Hurricane Harvey was followed by the powerful storms Irma, Jose, and Maria. Heatwaves and drought around the world, from India to Italy, have also brought misery and even death to millions.

When extreme weather strikes, lives and livelihoods are ruined, infrastructure destroyed, landscapes altered (sometimes irreversibly), and communities are often left with long-term mental and physical trauma. This clearly is a challenge not just for developing countries, but also for highly industrialised nations like the United States.  What can we do about this?

Beyond avoiding the most devastating future extreme weather by curbing greenhouse gases improving forecast capabilities and capacity provides some of the best defence. National and local decision makers require reliable warnings to be able to provide emergency planning and relief in their locally minded extreme weather action plans.

Nowadays, the most modern supercomputers, armed with a suite of state-of-the art models of atmospheric processes, generate higher and higher spatial and temporal resolutions with steadily improving forecasting skill. Progress in this ‘quiet revolution’ of forecasting is significant.1 But the next 10 years could yet see another huge paradigm shift in forecast capabilities.

A critical part of this drive for improved weather forecasting is the World Weather Research Programme’s (WWRP) 10-year HIWeather (High Impact Weather) project, a consortium of over 2000 scientists from diverse fields participating from institutions worldwide. I spent some time with Dr Paolo Ruti, global chief of the WWRP at the World Meteorological Organization (WMO) in Geneva, Switzerland, to discuss advances in forecasting extreme weather through HIWeather.

According to Dr Ruti, the ambition of HIWeather is “to promote cooperative international research to achieve a dramatic increase in resilience to high impact weather”. This will translate to saving more lives on the ground in the onset of an extreme weather event, both by improved forecasting capability and better communication to decision makers who activate plans to manage such potential disasters.

First, Dr Ruti took me through the technological and analytical aspects of improving extreme weather forecasting. This includes advances in the resolution of the forecast models themselves, which enable the latest weather models to include physical processes which are critical to predicting extreme weather.

A good example (among many) of improved resolution making a difference to forecasting capability is models which allow for resolving convection processes (drawing moisture for hurricane generation at scales less than 10km spatially) to take place. The newest models are showing remarkable realism in their simulation of the potential evolution of severe storm events for up to 15 days. This additional forecast lead time and accuracy will become invaluable when planning evacuation in cities during hurricane season.

Another key component of improving forecasts is identifying what in weather patterns may indicate the onset of extremes. This includes the work of Dr Hannah Nissan, a researcher at the International Research Institute (IRI) for Climate and Society at Columbia University, New York. Dr Nissan mainly works with developing countries in Africa and South Asia to develop and improve extreme weather early warning systems. She is an expert at extending the forecast horizon of warnings by finding novel sources of predictability.

Dr Nissan and the IRI have researched the predictability of extreme heat in Bangladesh.2 Nissan has explored patterns of air transport and soil moisture, and found “heat waves are preceded by a characteristic wind pattern in the atmosphere, which can set itself up about a week to 10 days before a major heat wave.” Not only that, but reliable warnings up to 30 days in advance may be possible because as ‘soils are drier than normal for at least a month before a heat wave on average.” This will be essential to plan mid-term action plans in response to destructive heat waves.

Beyond improving modelling of weather and its extremes, challenges include data collection to power numerical and physical modelling of weather extremes. Data from the ground weather stations is the fuel for forecasting extreme weather. Developing countries like Bangladesh, however, suffer from a lack of essential weather measurement infrastructure. Dr Ruti of WWRP explains that “data, and real-time observations are a key challenge” for this purpose.

To address this challenge, Ruti said “weather data is being crowd sourced through third party networks using apps or portable weather measurement devices.” An example Ruti highlighted was of the use of mobile phones as a proxy for radar measurements to monitor and forecast rainfall. A pilot project by the French Institute for Development Research in Toulouse has demonstrated a proof-of-concept system in Burkina Faso, Niger, and Cameroon.3,4 This type of technology could emerge as especially important in parts of the world with poor ground-based weather monitoring infrastructure. With high penetration of mobile phones in most of the world,5 it is a promising example of where the next generation of weather data collection and assimilation into forecast models lies.

However, using data from public sources isn’t as simple as plugging it in to a forecasting system. Ruti warned me that “understanding the error characteristics of these data will be critical to using them effectively.” Prior to data post-processing using mobile phone data, the readings of rainfall could be two to three times the real value. Data needs to be trustworthy and processed correctly before it is used for forecast outcomes. Yet, the work is a positive move away from the expensive centralised government weather measurement projects in places which cannot necessarily afford to maintain them.

Crowd sourcing contributions in the aftermath of extreme weather is also a growing area. A leader in the field is Zooniverse, the world’s “largest and most popular platform for people-powered research.”6 The crowd sourcing of over 10,000 contributions to observing the devastation of Irma and Maria from satellite data has resulted in a damage analysis of buildings all over the Caribbean in just a few days, which would have traditionally taken a single researcher over a year. Partnering with the Machine Learning research group at Oxford, Zooniverse have built a powerful mechanism to catalogue damage from extreme weather events, which is invaluable for the clean-up and rebuilding phase.

Zooniverse continues to be involved with identifying the damage caused by the devastating hurricanes of summer 2017, as well as the historical classification of cyclones to help further the understanding of patterns and potential trends of cyclones under climate change. While these are two independent projects, they both serve the broad goal of increasing understanding and preparedness for any similar future events.

This kind of work attracts a wide range of contributors (based on a 2015 survey), with a balanced distribution of ages. Currently, those actively participating are mainly from English-speaking countries, as a combined 64% originate from the UK or the USA, with only 2% from developing countries.  Many state that contributing to the projects on Zooniverse is fun, and that contributing to scientific progress is a strong part of the appeal.

Professor Brooke Simmons, Einstein fellow at UC San Diego, and leader of the Zooniverse Analysis Group, explains that the work users are doing on Zooniverse is a making a noticeable difference on the ground, with “really good feedback” from first responders, especially in response to Irma and Maria in 2017, where Zooniverse was called in to inspect the damage.

One such first responder, Rebekah Yore, of Rescue Global, an international Non-Governmental Organisation working to reduce disaster risk reduction around the world. Having previously worked on the response to Irma and Maria in 2017, Yore explains that Rescue Global could quickly find a set of personnel via Zooniverse whereby thousands of volunteers rapidly analysed pre- and post-storm satellite images to identify “specifically features of damage and hazard from infrastructure collapse, flooding and other causes”.

Once the volunteers’ work was done, the Machine Learning department at the University of Oxford would ‘run the responses through algorithms to filter anomalous results, improve the reliability of data, and produce heat maps of identified damage and features on the ground’. This became an essential component in Rescue Global’s humanitarian response, which was involved in determining which affected populations’ needs were the most critical, and which areas may have been more dangerous to traverse for teams deployed on the ground.

From a humanitarian response perspective, and particularly from the hurricane response in the Caribbean in 2017, Zooniverse allowed a great amount of accurate information to be generated extraordinarily quickly. Yore is quite clear that without Zooniverse, the first responders could not have had this kind of information to hand. Why was this information so useful? Yore sets the scene for what greets the those who are first to such disaster zones: “villages may have disappeared, there may be new, spontaneous groups of internally-displaced people. Bridges and access roads can also be destroyed, with flooding and landslides potentially blocking access”. The insights from Zooniverse are essential for both finding vulnerable populations while also protecting members of the rescue community.

Thus, arguably the most dramatic change to preparing for extreme weather is also how responses to them are managed. HIWeather has also identified endemic challenges of what a forecast should indicate, such as how to best spread effective warnings to a vulnerable community. Social media activity is a good way to analyse how effectively an extreme weather warning is being received and followed.7

While it is one thing to create experimental forecasting products; it is another to create something which decision-makers can use without requiring very specialised knowledge, often sorely lacking at Earth’s most vulnerable areas. Dr Joy Shumake-Guillemot leads the Joint Office for Climate and Health within the WMO, which specialises in translating forecasts into actions which local decision-makers can employ in extreme weather events.

Shumake-Guillemot recognizes how important it is to translate forecasting research into something useable for those on the ground: “the last-mile user (i.e. those who have to use the results for the purposes of minimising risk for vulnerable communities) in the ministry of health is often the neglected piece of the puzzle. Without building forecasting systems that factor in decision making, cutting-edge forecast products can so often become unused, especially in developing countries.”

Dr Ruti of WWRP also made clear to me that the key to saving lives and livelihoods is not only the forecasting technology, but also the methods of communicating the hazards to a community: ‘Better prediction and communication should go hand-in-hand’. We need to understand the ‘physical and social factors limiting the capability to communicate’, as well as understanding how to find better ways of forecasting.

A critical failure in the most devastating disaster to ever hit Myanmar, Cyclone Nargis in 2008, was that although the Indian Meteorological Office had predicted the extreme with four days’ notice,8 traditional methods of disseminating the warning (such as via TV and radio) did not reach isolated communities in the low-lying regions of the country, resulting in over 100,000 potentially avoidable deaths.

The link between decision makers and predictions often is at a disconnect, and this is the mid-term key to improving action on disaster forecasts. While events like Hurricane Harvey and others are truly terrible, they provide an opportunity to remind policy makers that it is critical we get the forecasting and communication coupling right. The future of forecasting includes targeted messaging to vulnerable populations, including the elderly, the young, prisoners, and labourers. Great gains can be made with existing technology and improved communication.

Of course, key steps forward in forecasting technology will occur over the next decade. But progress will not only develop in the models’ themselves, but also in the data collection for the models by crowd sourcing, and clarifying and communicating the forecasts to decision makers and then to vulnerable communities.

The future is full of extreme weather, but we can at least know a good deal more about it before it arrives.

 

 


References

1         Bauer P, Thorpe A, Brunet G. The quiet revolution of numerical weather prediction. Nature 2015; 525: 47–55.

2        Nissan H, Burkart K, Mason SJ, Coughlan de Perez E, van Aalst M. Defining and predicting heat waves in Bangladesh. J Appl Meteorol Climatol DOI:10.1175/JAMC-D-17-0035.1.

3        Tollefson J. Rain forecasts go mobile. Nature 2017; 544: 4–5.

4        Doumounia A, Gosset M, Cazenave F, Kacou M, Zougmore F. Rainfall monitoring based on microwave links from cellular telecommunication networks: First results from a West African test bed. Geophys Res Lett 2014; 41: 6015–21.

5         The World Bank. Mobile cellular subscriptions (per 100 people). 2017. https://data.worldbank.org/indicator/IT.CEL.SETS.P2?end=2016&start=1960&type=shaded&view=map&year_high_desc=true.

6        What is the Zooniverse? Zooniverse. 2017. https://www.zooniverse.org/about (accessed Sept 28, 2017).

7         Ripberger JT, Jenkins-Smith HC, Silva CL, Carlson DE, Henderson M. Social Media and Severe Weather: Do Tweets Provide a Valid Indicator of Public Attention to Severe Weather Risk Communication? Weather Clim Soc 2014; 6: 520–30.

8        IFRC. Community early warning systems. Guiding principles. 2012; : 84.

 


 

 

Who’s who in the Zoo – Philip Fowler

In the first of our new series of ‘meet the researcher’ blog posts, let me introduce Philip Fowler, who leads our Tuberculosis-fighting project, BashTheBug

– Helen

 


STJO_0130CM-square - Philip Fowler

Project: BashTheBug

Researcher: Philip Fowler, Senior Researcher

Location: John Radcliffe Hospital, University of Oxford, UK

 

What are your main research interests?

Antibiotic Resistance

 

Who else is in your project team? What are their roles?

I’m part of a project, CRyPTIC, that is collecting samples of tuberculosis around the world. So there are lots of scientists I’ve never met in labs in other countries who prepare the samples, inoculate the plates and take the photos that ultimately end up on BashTheBug.

 

Tell us more about the data used in your project

All the photographs you see are for a series of wells containing a single antibiotic. There are a few with 5 or 8 wells, but most antibiotics have either 6 or 7 wells. As you head from left to right, each well contains double the amount of antibiotic as the one before. Each strip of wells has been cut from a single photograph of a 96-well plate that contains 14 different anti-TB drugs in total. And each plate has been inoculated with a sample of M. tuberculosis taken from a patient somewhere in the world and incubated for two weeks. We hope to process 30,000 plates which means 6.3 million classifications over the next few years…

 

How do Zooniverse volunteers contribute to your research? 

They help us by deciding in which wells the bacteria are growing (and therefore the antibiotic isn’t working) and which wells they don’t grow.

 

What have been the biggest challenges in setting up your project?

Umm, writing the software that cuts up each photo of a 96-well plate into smaller images for uploading to the Zooniverse.

 

What discoveries, and other outputs, has your project led to so far?

Our volunteers have found some artefacts that we completely missed. One person spotted fuzzy patches in the last well for one drug; turns out this is the drug clofazimine crystallising in the bottom of the well as it is present at such a high concentration!

BashTheBug won the Online Community Award of the inaugural NIHR Let’s Get Digital competition back in August 2017.

Having shown the project to lots of people what has been really interesting is it ends being a test of how optimistic or conservative you are; people who are the latter will say any small spot they see is bacterial growth, whereas the former tend to say “nah, that is really small so I am going to ignore it”. Fortunately we are asking enough people that this averages out!

We are currently trying to work out how to best build a consensus from all the classifications our volunteers have done; watch this space. Anything we do intend to publish we will first submit to the biorXiv so volunteers will be able to freely download our manuscript.

Oh, and someone mentioned us in a poem.

 

Once you’ve finished collecting data, what research questions do you hope to be able to answer?

A subversive one: is a crowd of volunteers more accurate and/or consistent that an expert?

A left-field one: which genetic mutations in M.tuberculosis confer resistance to certain antibiotics and, equally importantly, which do not?

 

What’s in store for your project in the future?

Beyond a lot more data? Hmm.

We’ve got a new design of 96-well plate on the horizon, also we want to pool all our data to see if using something like Zooniverse, but in a clinical setting, could be used to help deal with difficult cases in a hospital lab.

I’m also thinking of better ways to engage with the volunteers – more soon.

 

What are your favourite other citizen research projects and why?

I love SETI@home as it is a bonkers idea, has been going for about 20 years and was the inspiration behind the BOINC framework (https://setiathome.berkeley.edu).

 

What guidance would you give to other researchers considering creating a citizen research project?

Just try creating a test project, it is easier than you think!

 

And finally, when not at work, where are we most likely to find you?

On one of my bikes, or playing Minecraft with my two daughters.

 

 

Microscopy Masters draws to a close

The guest post below was written by Jacob Bruggemann, a graduate student based at the Scripps Research Institute, who helped lead the biomedical Zooniverse project, Microscopy Masters.

Read on to find out about the findings of this project, made possible by the efforts of our fantastic citizen scientist volunteers. If you would like to learn more, you can access a preprint publication about this work here 

 With thanks to Zooniverse Volunteer Becky Kennard for editing this piece. 

– Helen 

 

Microscopy Masters draws to a close

Microscopy Masters, the cryo-electron microscopy (cryo-EM) project building complex 3D models of proteins, is approaching its initial conclusion. Over the two years the project has been running, we’ve collected over 17,000 classifications and built a dataset of 209,696 unique protein particles. The primary dataset used in this project was the 26S proteasome lid complex generated by the Lander Lab at the Scripps Research Institute. We have also annotated other, smaller datasets.

The proteasome is a large multi-protein complex responsible for breaking down unwanted proteins into reusable parts, kind of like a large recycling center for the cell. Studying its structure could reveal the mechanisms behind how the proteasome lid only opens for proteins marked for recycling, and give insights into problems caused by the lid malfunctioning.

This project is centered on an important tenet in biology, ‘form follows function.’ On the molecular level of biology, what this means is that the shapes of large biological molecules, such as proteins and nucleic acids, are evolved to perform specific functions. By studying and understanding the structure of biological complexes, researchers can better understand how all the little moving parts of life interact, which will allow them to better combat diseases and disorders.

Scientists are often too busy in the lab to come up with catchy names, meaning that the techniques they invent are usually given pretty self-explanatory titles. In the case of cryo-EM, everything you need to know is in the name.

Imagine some scientists are interested in studying a protein, say our subject, the 26S proteasome lid. Cells containing large quantities of the protein are lysed (a scientific way to say ‘popped like balloons’) and the contents of the cells are put into a solution. That solution is purified so that it only contains the protein the scientists are interested in. The purified solution is then flash-frozen in extremely thin ice (cryo) and put under an electron microscope (EM) to obtain images of the proteins. These images are then put through sophisticated reconstruction software to obtain a detailed 3D model of the protein. This technique is so powerful, scientists can identify individual atoms in the protein complex, giving them deep insights into how it interacts with its environment.

nature19948-i1

Figure 1 A schematic of how cryo-EM is done. Taken from dx.doi.org/10.1038/nature19948.

Of course, there have been years of work involved in the cryo-EM that I just explained in four sentences (and some very, very expensive microscopes!). A particularly time-consuming task for cryo-microscopists is picking the individual proteins from the microscopy images (micrographs), called ‘particle picking.’

Scientists used to do this by hand, but since they often have thousands of these images to process, this can take weeks of work. So, they usually rely on software to extract the protein images. But because some proteins are so complex, it can be difficult for software to identify them in the noisy micrographs. For this reason, we decided to train citizen scientists to pick the particles from our proteasome lid data and see if it could be used to build a detailed molecular model.

picking

Figure 2 On the left is a blank micrograph, on the right is a micrograph that has had the proteins manually picked.

Using the data from our volunteers, we made a full 3D reconstruction of the proteasome lid. We compared the model to one made with an automatic particle picker, both of which are shown below. Although they look very similar, what matters for microscopists is the ‘resolution’ of the reconstructions. What resolution means in this context is how consistent the models are when used several times.

In this case each dataset was divided into two random halves and made into two separate models, which were then compared to determine a resolution. Even though the resolution for the computer-made model is lower (better) in this case, this is partly due to the fact that the computer-picked dataset had so many more particles. For this reason, we also did a reconstruction using a subset of the computer-picked data with the same amount of particles as the crowdsourced dataset. This brought the resolution to 4.036 Å, closer to the crowdsourced dataset but still lower.

refinements

Figure 3 The final reconstructions of the crowdsourced and computational datasets. The resolutions for each are listed, the lower the better.

Even with the higher resolution, we believe this is a fantastic example of the power of citizen science. We built an entirely hand-picked dataset from people who had little to no experience with cryo-EM. This dataset allowed us to build a detailed, 3D model of a complex protein that had a similar resolution to the one built by a team of trained scientists with state-of-the-art software.

This was the first time we have run a project of this nature, and we believe that with tweaking and better feedback systems (which were only implemented by the fantastic Zooniverse team late into our project’s run) we can process data better and faster than we did in our first run.

As a side experiment to try and figure out how to better engage users, some of our project’s participants might remember being sent newsletters about ‘sprint’ datasets, which were small datasets of 15-20 images of other proteins. The use for these was not to build an entire particle dataset, but to provide data for the researchers to feed their automatic particle picking software. We found that giving the images different color schemes than the traditional black-and-white was a nice way to ‘spice’ the micrographs up for users, and we were able to provide researchers with usable data in a matter of days that they could use to start their data processing.

Although we currently have put the Microscopy Masters project on hold, we are excited with the results and in the process of submitting a publication of our initial results. I would like to thank everybody involved with the Zooniverse for building a fantastic platform to try our project. In particular, I would like to thank the Zooniverse team for answering my questions and helping me get Microscopy Masters up and working.

And lastly, thank you to all the hard-working participants in Microscopy Masters and everybody who participates in this great website!

 

Find out more:

You can check more of the great work done here at the Su lab on our website.

The Lander Lab is consistently pushing the work being done in cryo-EM, go see the work they are doing at their homepage.

Our publication can be previewed as a preprint on bioRxiv.

 

 

Step into the Zoo

Dr Sam Illingworth, Senior Lecturer in Science Communication and Poet, wrote the following Zooniverse inspired poem for us; ‘Research for All’.

If you’d like to read more of his work, check out Sam’s blog here.

– Helen

Research for All

 

Detecting bubbles in the Milky Way,

Or sorting a muon and gamma ray;

Identifying planets and their stars,

Then codifying ice geysers on Mars.

 

From mapping out old weather lost at sea,

To counting jungle rhythms in a tree;

With floating forests hiding in plain sight,

Sometimes research just needs a brighter light.

 

Etching a cell to analyse their state,

And bashing bugs to keep drugs up-to-date;

The history of what has gone before,

Can help predict what science has in store.

 

Transcribing ancient texts and works of art,

Unearthing words that set Shakespeare apart;

Revealing secret lives and hidden gist,

By searching for what others might have missed.

 

In answering the questions left to find,

We need the help of more than just one mind;

A Universe of projects yet to do,

The door is open, step into the zoo.

 

 

 

Panoptes CLI 1.0, a command-line interface for managing projects

Following on from the release of Panoptes Client 1.0 for Python, we’ve just released version 1.0 of the Panoptes CLI. This is a command-line client for managing your projects, because some things are just easier in a terminal! The CLI lets you do common project management tasks, such as activating workflows, linking subject sets, downloading data exports, and uploading subjects. Let’s jump in with a few examples.

First, downloading a classification export (obviously you’d insert your own project ID and a filename of your choice):

panoptes project download 764 Downloads/pulsar-hunters-classifications.csv

cli-classification-download.gif

This command will optionally generate a new export and wait for it to be ready before downloading. No more waiting for the notification email!

New subjects can be uploaded to a new subject set like so (again, inserting your own IDs):

panoptes subject-set create 7 "November 2017 subjects"
panoptes subject-set upload-subjects 16401 manifest.csv

cli-subject-upload.gif

You can also pipe the output from the CLI into other standard commands to do more powerful things, such as linking every subject set in your project to a workflow using the xargs command (where 1234 and 5678 are your project ID and workflow ID respectively):

panoptes subject-set ls -q -p 1234 | xargs panoptes workflow add-suject-sets 5678

Visit GitHub to get started with the CLI today!

A Late Night at the Museum

At the end of October, The Zooniverse team was invited to the Natural History Museum in London to be part of the Museum’s monthly Lates event program.

(Photos courtesy of the Etch A Cell team)

The event was organised by the ConSciCom team who have partnered with the Zooniverse to create two very successful projects – Science Gossip and Orchid Observers. The theme for the evening was to explore the role images, such as illustrations and photographs, have played within natural history and scientific research.

From studying animal behaviour using photos taken by camera traps, to advancing our understanding of cell biology with photos from microscopes, many Zooniverse projects improve our understanding of the world around us through the help of citizen scientist volunteers.

Teams from multiple Zooniverse projects, including BashTheBug, Etch A Cell, Notes from  Nature, Orchid Observers, Science Gossip and Seabird Watch, attended the event and spent the evening speaking to people about their projects, and showing how anyone can contribute to real research through citizen science.

(Photos courtesy of the Etch A Cell team and Jim O’Donnell)

Illustrator Dr Makayla Lewis led a live gallery drawing event, asking visitors to pick up a pencil and spend 15 minutes sketching their favourite exhibits.

2017-10-27_22-00-28_130

(Photos courtesy of Jim O’Donnell)

Thanks to everyone who got involved, including Fiona (Penguin Watch), Freddie (University of Oxford), Jim (Zooniverse Developer), Makayla (Illustrator), Martin (Etch A Cell), Nathan (University of Oxford) and Phil (BashTheBug), and especially all our volunteers who attended the event!