Tuesday, October 23, 2018

Reference Database Helps Scientists Estimate a Person's Genetic Repeats

There are many ways in which our genomes vary from one another, leading to differences in various traits or disease susceptibilities. Most researchers who want to uncover these differences focus on simple “spelling” mistakes in our DNA.

“Yet there are complex, repetitive parts of our genome that are also known to cause diseases, such as Huntington’s disease, and these parts of the genome are not analyzed in most large medical genetics studies,” said Melissa Gymrek, PhD, assistant professor at UC San Diego School of Medicine and Jacobs School of Engineering.

So Gymrek and her team built a reference database that allows researchers to estimate a person’s genome at these repetitive regions, even when they are not directly measured.

“This resource will enable analyzing the effects of repeat variation for the first time across hundreds of thousands of individuals on thousands of traits without the need to collect any additional data,” Gymrek said.

Read more about this new resource and its applications in Nature Communications, October 23:

A reference haplotype panel for genome-wide imputation of short tandem repeats. 

Thursday, October 18, 2018

SD Hacks

By Kritin Karkare

Hackathon participants hard at work on their project. Photo courtesy of SD Hacks.

Rain and lightning didn’t stop nearly 800 students passionate about coding from participating in the fourth annual SD Hacks hackathon, held at UC San Diego and hosted by the Triton Engineering Student Council (TESC). The 36-hour event, which ran from October 12 to 14, is an intercollegiate hackathon where students from across the country come together to create innovative solutions to challenges or projects of their choice in a mere 36 hours. Sleep not included.

Albert P. Pisano, Dean of the Jacobs School of Enginering,
welcomes students to UC San Diego at the SD Hacks
opening ceremonies. Photo courtesy of SD Hacks.
TESC organized the event, which was sponsored by the Space and Naval Warfare Systems Center Pacific (SSC Pacific) and featured collaborations with student clubs like the Computer Science and Engineering Society (CSES) and other partnerships with companies and organizations like the Power of Neurogaming Center in the UC San Diego School of Medicine and Northrop Grumman Corporation.

This year, a total of 109 teams submitted projects to SD Hacks, ranging from a dog meme classifier to a search and rescue robot that could help emergency crews in dangerous situations. As with previous years, hackers could also participate in challenges set by SD Hacks partners, where projects can take advantage of APIs offered to win specific prizes. For example, DocuSign challenged students to create a project that made the best use of their e-signature API, with the winner taking home $2,000 and an interview for a job or internship.  Other services available included Google Cloud Platform and Domain.com. 

3, 2, 1... HACK! Photo courtesy of SD Hacks.
David Ding, a third year electrical engineering student at UC San Diego and director of SD Hacks, said that the hackathon took more than six months to plan. The most difficult part? Getting all the sponsors; their last one was confirmed in early October. His favorite part though, was the opening ceremonies because he got to see everything come together. To him, that was extremely gratifying. With the help of 135 dedicated student volunteers under his leadership, SD Hacks ran smoothly.  

Of course, coding 36 hours straight will do a number on the mind. Thankfully, UC San Diego is home to a beach just 15 minutes away, where students can go to relax if they need a break. 
Participants from other colleges liked that about UC San Diego. Kishan Sarvaiya and Kizar Cassiere from Long Beach State University both said that compared to other schools that they have gone to for hackathons, UC San Diego offered better things to do in terms of experience. 

After a long 36 hours, and almost two hours of judging, one group came out on top as the Grand Prize, Best Overall Hack winner for SD Hacks 2018: Polyglot. Polyglot’s team consisted of members Naba Rizvi, Yizhen Shi, Carla Marzari, and Jacob Perkins, all from the University of Toledo in Ohio. They developed a way for non-English speaking youth to learn how to code in their native language, since most programming languages use tags and keywords in English. Polyglot helps them both learn the English words, as well as learn how to code. 
To learn more and try out Polyglot, check out their DevPost here: PolyGlot

To check out the wide scope of project submissions, click on the link to the SD Hacks DevPost

Tuesday, October 2, 2018

Engineers on the Green highlights diverse student organizations

By Kritin Karkare
More than 400 students attended TESC's Engineers on the Green.
Photos by David Baillot. 

On a cloudy afternoon on the first Monday of Fall Quarter 2018, members from all of the engineering student organizations filled Warren Mall with their project demos, sign-in sheets and informational posters waiting to recruit incoming and returning students at this year’s Engineers on the Green. The annual event is organized by the Triton Engineering Student Council (TESC), which hosts Engineers on the Green to help engineering organizations get greater visibility and recruit interested students for their club activities. The event drew nearly 800 students and continues to grow each year.

The event played host to about 50 different engineering clubs from a wide breadth of disciplines.

Are you interested in pitching your engineering project ideas and getting funding for them? Divergent Engineering has helped projects like a stair climbing robot get sponsored by Qualcomm.

Triton Racing, Tritons for Unmanned Aerial Systems (TUAS), and Design/Build/Fly (DBF) have exciting opportunities to expand mechanical engineering, electrical engineering and computer science skills, with members working on race cars, autonomous drones and RC planes, respectively, that compete in annual competitions.

If you want to apply your engineering skills to communities outside of campus, learn more about Engineers Without Borders (EWB): some of the projects EWB works on include a water filtration system in communities in Kenya and in Tijuana.

And those are just a few of the project-based groups. Many of the engineering organizations also focus on professional development, outreach, and event planning meant to promote interest in engineering. For engineers that want to get help in soft-skill building and industry relations, they can join the International Society for Pharmaceutical Engineers (ISPE) for their leadership rotation program and their industry mentorship program.

Want to bring STEM education to young students? Look no further than Tritons for Sally Ride Science. They host workshops for kids like “Science of Harry Potter Magic” and Ignite Talks to inspire even undergraduates to look for new opportunities in their fields.

Lastly, the Nanoengineering and Technology Society (NETS) works on events like the Nano Day Conference to develop interest in nanoengineering and hosts projects for skill development.  

The wide range of opportunities is staggering, whether it be in project-based work or professional development. For more engineering organizations not highlighted, take a look at TESC’s list of organizations here.  

Monday, September 17, 2018

ThoughtSTEM, company founded by UC San Diego alumni, receives $330k grant from National Science Foundation

ThoughtSTEM, LLC, a San Diego-based company teaching computer science skills to students ages 5 to 18, has received a $330,000 Small Business Innovation Research grant from the National Science Foundation. ThoughtSTEM is most well-known for being the first company to release a Minecraft Modding software, LearnToMod, that allows kids as young as 5 to reprogram the popular video game, Minecraft.

ThoughtSTEM is led by UC San Diego computer science Ph.D. alumnus Stephen Foster and biochemistry PhD alumna Lindsey Handley.

“Thanks to the NSF, we are now going to be able to reach more students in different countries with different interests," Handley said. "The same experience students have had in our classrooms will soon be available online to both students... and adults. We're really interested in sharing our educational tools with more adults so they can help us reach more kids.”

With this new grant funding, ThoughtSTEM will able to offer more of their innovative, video game-inspired computer science curriculum to students around the world by moving online the curriculum they've been using in classes with students in San Diego. There will also be a push to develop a completely new computer science curriculum designed to meet the interests of a broader population of video game-playing students worldwide.

The mission of ThoughtSTEM is to find every student interested in understanding how computer programming works and teach them in a context they can understand - video games. ThoughtSTEM has taught over 7,000 students in San Diego and over 100,000 students online.

This grant is allowing us to accelerate our development of computer science educational products for students who we are looking for new ways to interact with their favorite video games," Foster said. "Our students in San Diego have really enjoyed our approach, and we are excited to now be able to share it with other areas.”

ThoughtSTEM also was co-founded by computer science Ph.D. alumna Sarah Guthals, who now works at GitHub.

Friday, September 14, 2018

10 Things to Know Before You Start Engineering at UC San Diego

Antonio Sanchez, a professor in the department
of mechanical and aerospace engineering,
researches chemically reacting flows.

Antonio Sanchez, a professor of mechanical and aerospace engineering at UC San Diego and an alumnus of the Jacobs School of Engineering himself, gave incoming freshman in the Summer Engineering Institute some pearls of wisdom as they begin their engineering careers. He and some of the graduate students in his lab put their heads together to create a list of 10 things that new Jacobs School students should know, and the advice is too good not to share. So, without further ado:

10 Things to Know Before You Start Engineering at UC San Diego

1)      Be proud. Living in San Diego, we have the sun and weather and can take for granted that we have UC San Diego here. UCSD is one of the best universities in the entire world. The Shanghai Ranking [Academic Ranking of World Universities] lists it as No. 15 in the world. Then certain fields like mechanical engineering, my department, is ranked No. 4 in the world-- you get an idea of the place you are in.

2)      Be prepared. College is hard. It’s different than high school—you need to learn at a different depth. And the pace is different—UC San Diego is on a quarter schedule, so you only have 10 weeks. If you fall behind, there’s no way to catch up.

3)      Go to class. There are many good reasons why you should do that—your parents or you are paying for it. But there’s an even more important reason: as engineers, the rest of your life will be a nonstop process of learning. The big difference is now, here, there will be someone telling you what’s important and what’s secondary. Once you graduate you’re on your own and learning becomes much harder. You have very educated professors trying to teach you things—go to class, really.

4)      Don’t take shortcuts. The engineers who are building airplanes, bridges or computers, they don’t cheat. If they did, the airplane or whatever would fall. Please don’t cheat. Do the honest work. It’s much better to get a ‘C’ than to cheat. Be professional and you’ll be treated as a professional.

5)      Be patient. I was looking at your projects and it’s clear you will be great engineers one day. You’re here to build new cars, new engines, new computers, new software…. But the truth is you’re not going to see much of that at first. It’s all going to be math and chemistry and fundamental science. And at one point you might be wondering why it is that you’re not building airplanes? You’ll get there. Those building blocks are really necessary to make sure you learn in depth.

6)      Make the most of these resources. You’re paying a lot of money, and UCSD has these labs and computers and I think one thing students don’t use that much is office hours. An average professor charges between $500 and $1,000 an hour as a consultant—that’s free to you! You have someone waiting in their lab or office to meet with you—go ask questions. And TA’s have office hours too and are sometimes more knowledgeable on the course than the professor. Go to office hours, you’re paying for it.

7)      Who do you want to be in 10 years? That’s a key question. Take some time and think about that. Do you want to be working for SpaceX, want to be a professor, want to be a researcher in a national lab? Think about that, and then plan accordingly. You can shape your profile in these four years—be whoever you want to be. Don’t go for the easy ‘A’, go for what really interests you. It may be harder, but one day when you’re being interviewed by a company you’ll be able to tell them why you’re different and why you chose your path. Join a club to build this profile, too. And if there’s nothing that interests you, then create your own club. Think about who you want to be in 10 years.

8)      Broaden your horizons. There is life beyond engineering. For electives, most people do something easy. I say challenge yourself—take Chinese, take sign language, study medieval history, whatever. Do something out of your comfort zone. Study abroad—we’re making an effort to make those programs more accessible for you. By my accent you know I’m from Spain, but I studied abroad as well and it really changed my life. You get to challenge yourself these four years, so broaden your horizons.

9)      Embrace a professor. One day you’ll need a professor to write a letter of recommendation, so take time to develop a relationship with a professor. That’s important to your future success.

10)  Have fun! Remember that you’re here to get an education to become an engineer, but you’re surrounded by beautiful, brilliant people, so socialize. Don’t forget that. At the same time, you’re an adult—you have to be responsible. Be safe.

Friday, September 7, 2018

Summer Engineering Institute final projects

More than 100 incoming freshman participated in the five-week residential Summer Engineering Instititue at the Jacobs School of Engineering this summer. The students took courses that count toward their degree, received support in transitioning from high school to college-level curriculum, familiarized themselves with the UC San Diego campus, and made friends, all in short order.

The second part of the Institute, run by the IDEA Engineering Student Center, included designing a hands-on final project in teams. The students demonstrated their projects to family, friends and peers at a closing ceremony on Sept. 7.

Here are just a few samples of the projects the incoming freshman students were able to conceptualize, design and build in less than three weeks.

Project: Sleep Apnea Tracker
Team: Clare Zhang, Jane Earley, Aileena Wen, Dora Ogbonne

The sleep apnea tracker uses an accelerometer inside a small case worn around the chest to monitor the user's breathing. If motion exceeds a certain threshold, it registers as breath. If no breath is taken within a 10 second period, the device alarms and buzzes, waking the user and alerting them that they stopped breathing normally.

Project: Directional Sound System
Team: Steven Rojas, Joel Yow, Branson Beihl

Microphones attached to small wrist and back straps monitor noise, and buzz when they register noise over a set level. This lets the user know that they need to pay attention in the direction of the buzz. The system is useful for anyone hard of hearing, or for those listening to music or wearing headphones who may not hear ambient sounds they need to react to.

Project: LED Bed
Team: Jonathan Trang, Matthew Gao, Isabelle Del Rio, Mayci Marquardt, Michelle Singer

The LED Bed is a night light that shines from under the user's bed, triggered by a pressure sensor. Instead of disturbing roommates or children by plugging in and turning on lights, this night light knows when the user is in or out of bed based on weight. It can be timed to go on for a certain number of minutes-- if the user gets up to go to the bathroom at night, for example, it will stay lit for 10 minutes, and automatically turn off after that. A light sensor in the Arduino will shut off the device during the day.

Project: Guitar Tuner
Team: Julianna, Rafael, Jake, Kyra, Eden

The guitar tuner listens for the selected frequency, and LED lights glow the indicated color when the correct frequency is detected.

Project: Iron Man hands-on kit
Team: Samuel Figueroa, Carl Villegas,
Guillermo Nogueira, Daniel Aguirre

These students built two glowing Iron Man hands and a face mask as part of a do-it-yourself kit. The 3D-printed components have accelerometers inside, so the embedded lights glow when the hands or face move. Buttons-- programmable in Python-- allow for different pulses and colors of light to shoot from the hands and eyes. The students created this kit to be a hands-on activity to help children engage with engineering principles.

Project: Anxiety Detector and Reliever
Team: Alex Lazaroiu, Joseph Liu, Marcus Milton, Ryan Wing

This wearable device monitors the user's heart rate, calibrating to his or her average beats per minute. The LED lights glow red if the heartbeat exceeds a certain threshold, since elevated heart rate is one sign of anxiety. The lights on the device then blink in time with a slower breathing pattern-- the user tries to sync their breath with the lights to calm down. The device turns green when they've returned to their normal heart rate.    

Friday, August 31, 2018

COSMOS Week 4: final projects

COSMOS is a four week summer science and engineering program focused on teaching motivated high school students topics rarely seen in high school curriculums. My name is Kritin Karkare and I’m a bioengineering undergraduate student at UC San Diego, a former COSMOS Cluster 8 (Tissue Engineering) alumnus, and current Cluster 7 (Synthetic Biology) teaching assistant.  

For the four weeks of the program, I covered COSMOS life as a teaching assistant through this blog.  In the first post, I covered an introduction to COSMOS and interviewed Dr. Charles Tu, the UC San Diego COSMOS director. In the second I interviewed several students and shared some of my thoughts as a cluster assistant. The third week focused on the professors’ perspectives, and this week I am putting the spotlight back on the students through their final projects. In addition, I have some thoughts on my work in COSMOS. 

Cluster 6 final project:

Project: Volatile Gas Formation in Algae Formation
Members: Ricardo Ozuna, Brian Fang, Rosa Golchin and Bavan Rajan.  

Cluster 10 final project:

Project: Humanoid-Surveillance Robot
Members: Margaret Peterson, Skyler Stetson, Aishwarya Gunaseelan


For anyone who read through all four articles, thank you! Teaching for COSMOS is one thing,
but writing about it for others to experience is another. I am glad I could provide some insight
about this program through my unique lens. When I first came into COSMOS as a TA last year,
I was frightened; it was my first time helping to teach, and there’s nothing scarier to a new teacher
than being asked a question that you can’t answer! 

Students, and in particular high school students, asked insightful questions outside of lecture
material that often would push me do outside research to find answers. Maybe it was just me,
but I think starting my teaching experience in COSMOS and not in the college classroom was
the best choice. If it weren’t for the students’ smart, novel - sometimes ludicrous - questions,
I’m not sure if I would be as motivated to learn how to teach more effectively.
In his interview, Charles Tu, director of COSMOS at UC San Diego, referenced the sheer
curiosity high school students have compared to college students -  they ask more questions,
and more importantly, more “impossible” questions. From my personal experience in a college
classroom, I believe this as well. The COSMOS students showed me that there’s still this great
potential from curious students like them that just needs to be nurtured with the right environment.
As an example, I think COSMOS’ mix of science communication practice, hands on experience,
mentorship from professors and its commitment to encouraging failure is a paradigm to model -
particularly because I gained an appreciation for the rigor of the scientific method after going
through the lab process. 
Admittedly, this job shows me just how little biology I know, even after studying it for two years.
For their final project, one group asked if it was possible to make glowing yogurt, which made
my head turn. It’s not a scientific inquiry that most people normally ask at the undergraduate level
and above. However, it is the silly, and ultimately ambitious questions like these that drive science
and engineering advancement. Why not be bold? You might fail, but then you have more things to
experiment on, and that’s the beauty of science. The process never fails to entertain the mind of the

For these reasons, I’m glad that programs like COSMOS exist in order to let these young minds go wild. It’s not just the exposure to high level content; you can get that online easily without setting foot in a classroom. It’s empowering them with the tools to run their creative experiments, letting them feel disappointed when their hypothesis was wrong, and pushing them to keep going.  
As for me, I also gained something important from the students’ willingness to ask questions: a drive to motivate young scientists to keep asking good questions and to keep them coming fast. 
I want to thank the Jacobs School of Engineering for allowing me write and publish these blog posts. In addition, thank you to COSMOS for giving me the chance to be involved as a participant and teaching assistant, and finally, to Cluster 7 (Synthetic Biology) for the opportunity to be part of their community and engage the next generation in scientific discovery!

P.S. If you’re curious, there’s no consensus on glowing yogurt yet. While it seemed like the yogurt glowed, analysis of the sample a day later showed no glowing. Maybe that’s a final project to investigate next year?