Archive for the ‘app’ Category
The gamification of data analysis in cancer increases citizen contribution and reduces research time
Individuals diagnosed with muscle-invasive bladder cancer face a difficult treatment decision – intensive radiotherapy or complete surgical removal of their bladder. Each option has benefits and draw backs, and there are limited data available to patients and physicians to help predict which treatment might provide the best outcome.
Dr. Anne Kiltie, Associate Professor of Radiation Oncology at Oxford University and Clinical Group Leader at Cancer Research UK (CRUK) is trying to improve that decision making process. She is investigating whether proteins involved in DNA damage signaling and repair might serve as biological indicators, or ‘biomarkers’, predictive of a patient’s response to treatment.
In 2010 her team published data showing that higher levels of the DNA repair protein MRE11 correlated with better survival rates in bladder cancer patients who had undergone radiotherapy. This was a critical finding suggesting that MRE11 could be a treatment predictive biomarker. Unfortunately the finding relied on time consuming pathology analysis. Bladder tumor samples are sliced, labeled for each protein of interest and photographed. While the staining and imaging of these slices can be automated, each image must be manually quantified for the level of protein present. Computer algorithms are not yet as reliable as the human eye. So to study just one protein, Kiltie’s team must individually score hundreds of images, a major time sink.
Of course if there was a way to get more people involved, the research could proceed much faster.
And this is the basis of Reverse the Odds, a mobile app game in which citizens help with real data analysis. The game was the result of CRUK’s partnership with British television broadcaster Channel 4 and developed in collaboration with Chunk, Maverick Television, and Zooniverse.
“Developing this game was a new experience for both our researchers and the game developers,” says Rupesh Robinson-Vyas, Science Engagement and Operations Officer at CRUK. The development team had some key concerns. Could a game that dealt with a serious topic like cancer still be approachable and fun? And could the data analysis be gamified without compromising the quality of analysis?
Yes and yes.
The final product is a puzzle game in which players help whimsical creatures, ‘Odds’ reclaim their world. Rather than hide the science, the game developers put the science front and center. To level up, players visit the ‘lab’ where they learn to quantify protein expression in real bladder tumor samples. All the samples are from patients who have already undergone treatment. Players are not diagnosing patients.
Each image is reviewed by multiple players, with each player’s response being compared to other players’ responses. In this way discrepancies in analysis are weeded out. After the images are quantified, the data are sent back to Kiltie’s team who compare the level of protein expression to the patient’s known outcome.
Not only has the game cut down on data processing time, Kiltie’s team can concurrently evaluate the expression level of multiple proteins. This means the relationships between proteins, how they might work together to affect treatment outcome can also be studied.
As for the seriousness of the subject matter, rather than a deterrent, the science and the potential to make a significant contribution to cancer research is a strong motivator for game play.
“It was an unexpected outcome. The game allowed us to engage a younger age group, individuals who might not be able to contribute financially, could instead contribute their time,” says Robinson-Vyas. The game has been a huge success, translated into five languages, with an international reach of 150 countries.
CRUK is testing new methods of training and presenting pathology data to users. “Rather than asking our users just one question, the new interactive will teach us how to ask questions and identify what kind of data our users can help us collect,” says Robinson-Vyas. Results with citizen scientists matching pathologist’s accuracy in data analysis are encouraging; CRUK is writing a paper on these methods and plans to test further iterations.
As for Reverse the Odds, Kiltie’s team hopes to complete data collection this spring. Her team intends to make the results as well as background on game development openly available.
Visit the project page to learn more about Reverse the Odds and join the effort help Kiltie’s team analyze the final 500,000 slides by March.
Learn about CRUK’s other project Play to Cure: Genes in Space
Calling volunteers! Cancer Research UK has a new project called The Trailblazer Project. The goal is to develop an app that improves how users analyze cancer pathology data. Volunteers to help test the prototype.
The Cancer Research UK’s Citizen Science team is committed to finding innovative ways to accelerate research by crowdsourcing. Already, the team has three web-based projects up and running. Their new project channels the success of their earliest app Cell Slider. Cell Slider asked participants to identify cancer cells from healthy cells. The team found the public was able to identify cancer cells with a promising degree of accuracy. Now they are developing a new analysis mechanic which will allow for even greater levels of accuracy.
Early beta testing by pathologists and volunteers showed promising levels of agreement. The final iteration of the new mechanic will be ready for testing by volunteers in early August. Testing involves looking for cancer cells in tissue slides rendered into images on an online platform. Each image is divided into 12 sections, and testers click on regions they suspect contains cancerous cells. The team needs at least 30 volunteers to help with this final round of testing.
Once finished, the analysis mechanic will be made available either as a web-based app or a mobile game. This is a unique opportunity for volunteers to not only learn about cancer but to be directly involved in project development. Register to volunteer by emailing your full name to email@example.com.
As part of SciStarter’s regular radio series with WHYY’s The Pulse, we highlight new developments in citizen science and a few projects ripe for spring!
As the weather starts warming up and we all begin shedding our thick, winter coats, a crop of new citizen science projects are enticing us to get outdoors in the name of science.
Darlene Cavalier, founder of the citizen science website SciStarter and regular Pulse contributor, says a top project this spring involves paying attention to phenology, or the life cycle changes of plants and animals.
“This might be changes in the nesting habits of birds, certainly in the leafing cycle of plants near you and, specifically, looking at the timing that your lilacs bloom and when they die,” says Cavalier.
All of that information is connected in the sense that birds tend to time their nesting habits to when insects will likely be around to feed their baby birds. And those insects are dependent on certain plants to be around to survive.
Cavalier says the information that’s collected through this phenology project will eventually help inform climate assessment acts in the U.S.
As part of the Philadelphia Science Festival in April, the SciStarter crew will be at the Schuylkill Nature Center in Roxborough to get people involved in the Zombee Watch project.
“We have zombie flies that actually infect honeybees and we’ll tell you how to look for that,” says Cavalier. “It’s pretty disgusting and it’s also eerily attractive for some reason.”
But Cavalier says not all scientific research has to happen outdoors.