In Search of an Academic Research Data Management Tool to Rule Them All

I have been struggling with keeping track of various research projects and their progress, documenting failed experiments, processing the deluge of incoming sequencing data, managing the various local and international collaborators, and detailing the methods and parameters used to aggregate, analyze, and work through versions of manuscript within in the laboratory and with collaborators. This is particularly challenging as new projects come online and you and your collaborators have to keep track of incoming data and the evolution of data tools and analysis methods.GitHubEducation

In comes Git / GitHub and Bitbucket. I’ve stayed away from these because frankly, I don’t understand them and the learning curve scares the bejesus out of me. But I’ve been on vacation and spent some time reading about GitHub, their GitHub Education Program and the many opportunities available for collaborative sharing of experimental protocols, data, and analysis. Through this program, I have the ability to track progress through the various stages of experimental design, data collection, and analysis of results while also preserving data privacy and confidentiality through the use of private repositories.

The most interesting and exciting part of GitHub is the ability to track and compare changes over time while maintain detailed records of the multiple parallel tracks my science takes on my journey from hypothesis forming through manuscript submission and revisions. Will GitHub be applicable for every project? For interactions with every collaborator? Probably not. But it seems a good place to start.

Space, Mars, and the Desire to Explore

We choose to go to the Moon … We choose to go to the Moon in this decade and do the other things, not because they are easy, but because they are hard; because that goal will serve to organize and measure the best of our energies and skills, because that challenge is one that we are willing to accept, one we are unwilling to postpone, and one we intend to win …

– President  John F. Kennedy, September 12, 1962

I always dreamt about becoming an astronaut. Floating through space. Colonizing Mars and planets beyond. The early 70’s were a heady time for space travel. Disney World had just opened with it’s futuristic Tomorrow Land. We had Tang, Omega watches, dome houses, space day at school, and many other items that worked their way into our daily lives.

I remember the Apollo Space Program. I was living in Orlando, FL at that time. We could see the launch from our house. We would watch on TV at my grandparents house and then run outside every time a rocket took off, trying to be the first one to spot the rocket.

My parents and grandparents would take us to Kennedy Space Center where we would eat ‘Astronaut Food’. As kids, we loved the ice cream. In those days we could get very close to the launch pads. Below is a picture of me and my sister with our father in front of the Apollo 16 launch pad.

Apollo_16_on_launchpad

Apollo 17 would prove to be the last trip that the US took to the moon. It would be years before the Space Shuttle program was launched and a human crew traveled back into space. We never went back to the moon. The dream of going to Mars was put on an indefinite hold.

Now, I live in a country that dreams and believes it can and will go to Mars. That it will explore: boldy go where no one has gone before.  You can feel the excitement in the air. I may not be able to make it to space, but at least I now have a chance to continue that dream and help others get to and colonize Mars.

Environmental Sensors

I have been thinking of how to measure data in our upcoming field tests for the soil regeneration project. We need to be able to monitor several environmental parameters during these tests, such as temperature, humidity, light intensity, soil moisture, etc. We also want to be able to do this remotely, either with a wireless setup, a gpms shield, or RFID sensors, and be able to store the data onsite for future use. I stated thinking of how to do this best, so I did some research and it seems that using an Arduino / Raspberry Pi using Dragino or XBee style setup will probably work. Stay tuned for progress.

Extreme Environmental Sampling Wanted

Living in a desert can be a daunting experience. I am slowly acclimating to the heat in Abu Dhabi. I cannot last more than 30 minutes out in the summer sun. The temperature hovers between 45°C-50°C during the mid day. The humidity is high and shade is scarce.   But life has evolved to exist and even thrive under these harsh conditions. One such place is the tidal flats along the Abu Dhabi shore. Every high tide brings a fresh influx of sea water that evaporates during the interceding tidal cycles. Salt crust marks the receding high tide.

Looking over the mangroves
Looking over the mangroves near Yas Island.

Stopping on the road, I venture over the railing, walking down the embankment. The heat at the waters edge overwhelms me. The smell of salt and bitterness is in the air. I am surprised at how clear the water is. Small fish and crabs scamper away. I dipped my fingers into the hot water and watch as they dry, leaving a white crust on my skin. Supersaturated 45°C salt water.

shoreline_2
Looking down at the water’s edge

Standing on the shore, I think of how to get access to this area for environmental sampling. It will be exciting to investigate what microbial communities inhabit these salt flats.

Home, Sweet Home

Our Villa in Khalifa City A
Our Villa in Khalifa City A

All the looking has come to an end. One place we loved had no electricity; and no sign of it coming on in the near future. Another place was taken right from under our feet. We walked into the compound and it felt right. The I’m glad to come home here kind of right. We put the offer in. They said yes. Their people talked to my people. I picked up the keys today. Tomorrow we move in. Finally, the Don is home. Sweet home.

To Infinity and Beyond

We are officially expats. The movers showed last Monday and packed what was left of our belongings into neat symmetrical boxes all cataloged and labeled. A snapshot of where our life stopped in Boston ready to be picked up 6 weeks later in Abu Dhabi. As the plane taxis down the runway and the wheels lift off the ground I am filled with excitement and fear.

expat_sm
Off to Abu Dhabi

This has been my home for the last 11 years. Boston has been the place where I laid down roots. I ‘grew up’ here as you might say. Some of my biggest challenges and greatest successes happened here. I came here to graduate school at MIT. In the Chemistry Department. I did not realize until after the fact how grueling that would be. But it was also immensely rewarding. MIT allowed me to hang out with some amazing people from around the world. I dissected life and science with exciting people driven to change the world one invention at a time, developed great mentors, and have made lifelong friends from all corners of the world.

I met Lily at MIT. She changed my life. For the better. Now we are both off to London. Together. Eight days to contemplate our new life and prepare for our next adventure. Abu Dhabi.

To infinity and beyond.

A Tale of Two Cities Planned

I traveled to Orlando this week to visit my mother. I had known that the ‘urban development’ squad had severely affected the area, but it did not prepare me for the barren landscape I encountered. Gone were all the small shops and lunch counters. The streets were now 4-6 lane wide auto mobile conveyor belts with no chance that those ferried would slow down and drop out to frequent local shops on their way in to work and return their McMansions on the outskirts of town. This urban renewal planning fiasco slowly choked the life out of the small towns that developed around Orlando proper over the last century. Everywhere you turned there were empty corner lots, decayed structures boarded up with lease signs and no sign of a heartbeat of what once had been a vibrant small community. Over 50 years of politically based decision and bad planning had reduced once vibrant communities such as Eatonville, Winter Park, Maitland to a shell of their former selves.

An empty coner near Eatonville Fl
An empty coner near Eatonville Fl

 

As I drove (there is no way you could get out and walk) through these communities it was not hard to be overrun with a feeling of tiredness and despair evident the recent attempts to reconstruct what was left of these towns. One word came to mind – Disneyfication – an attempt to reconstruct these run down communities into a cookie cutter facsímile of the Disney pseudo-utopian Celebration City. There is no sense of the lived in by the living in and around the reconstructed streets.

Later, as I sat in my mother’s house I started to think about the contrast between the city I grew up in and the city I am going to see grow up in Abu Dhabi, Masdar City. A gruesome, tortured urbanization compared to a well thought out urban space that reinforces a dense population and community space. A city developed by Sir Norman Foster on the combination of the Arab understanding of physical and social structure wrapped in 21st century construction materials and technology. A place purposely built for human inhabitants to move around and interact free of metalic machines grumbling along concrete superhighways.

So long MIT

 

Mens et Manus
Mens et Manus

This week marks the end of my time at MIT. When I leave on Friday, I will have been here for 10 years, 11 months, and 16 days. 4002 days. It is had to imagine that I have been here for this long. I remember showing up to Tang Hall and getting my room. Up in the corner of the 24th floor. Now, I have a PhD – 8 years in the making, three years of Post Doctoral work, and I met one of the most amazing people in the world, who agreed last year to spend the rest of her life with me.

Along the way, I have met some incredible people. Jarrett, who officiated our wedding and has been there every step of the way since our beginning. Kerry, who came with Lily and has been an amazing friend. Eric and Zary, fellow MITers whom I kind of brought together (at least that is the story I am telling). Charles, for those out there and realistic conversations on the pursuit of science and scientific thought. Peter, who I can always count on to get things done. Will, who has been a true and loyal friend for some long years now. John Essigmann, who has been a terrific mentor and friend to me. Joost, who always plied me with libations and conversation. And many, many more. Too many over the years to recount here.

Lily and I are leaving soon, and arriving later this month, at Masdar Institute a brand new graduate research institute in Abu Dhabi. I will be a Professor in the Chemical Engineering Department.I am excited about the opportunities ahead of me, but also mindful of the responsibility that comes with this opportunity. It will not be easy, but it will be very rewarding.

It is not a good bye, but a so long to MIT and Boston. We will be back soon.

Standing on the shoulders of giants

I was reminded of this phrase while at dinner this week. I recently became a Dr. Martin Luther King Jr. Visiting Scholar at MIT. As part of this honor, I was invited to attend the Faculty of Color monthly dinner. I must admit I became more nervous as the day of dinner approached. Most of these Professors I interacted with while a student representative on a Faculty Committee in my role as a graduate student representative. Some I had only read about while studying the history of the Minority Community at MIT. All of them are leaders in their respective fields of research and contributors to the advancement of Minorities in Academics.

As I sat there listening to their stories at dinner, I reflected on how much they each gave in their own way to open doors for my generation. Reading their history paled in comparison to hearing the narrative in person. It is hard to gauge the thought process from the written word. To glimpse into environment from which decisions were made. Whether thirty years out, it was all worth it. Being there at the dinner, listening to the changes in inflection, taking in the hand gestures, and observing the shifting body language lent a sense of reality and depth to the narration that is absent in the written word.

I cannot imagine the strength and resolve it took to put up with spitting, cigarettes butts, sleeping in isolated conditions, or being ostracized from the academic community because of what you were not. All I know is that I am thankful to them for the road they paved for me.

Later that evening, while on the Red Line going home, I realized that at one time, they were just like me. A potential to be used. The choice on how that potential was to be used was mine and only mine to make. Only time would tell, but if I choose to do what I believe and do not compromise, it will all work out. Just then a song came into my head; REM’s ‘King of Birds’ lyrics, standing on the shoulders of giants, it leaves me cold. As I hummed the tune, I smiled knowing that although it is going to be a hard endeavor, it will not be impossible. They made sure that I have more than a fighting chance.

Fall is here; faculty job search begins

The first hints of fall are in the air. The cool evenings herald the end of the summer and the beginning of the fall. What a summer it has been. I married the love of my life and we traveled to London, Tanzania, and Zanzibar in a three-week honeymoon. Africa turned out to be all that it was purported to be, enchanting Lily and I. We know that this will not be the last time we visit.

Now that summer is coming to an end, a new season begins. Most of you will think of fall and of leaves changing. In some sense I will be thinking of that too. But the fall also means the beginning of the faculty search cycle. This year I will be joining that cycle. There are many things that need to be done. Proposals are being written and rewritten, talks need to be arranged and prepared, and trips around the country are being organized. I have prepared for it, as much as I can, but it is still a daunting and foreboding path. I am stepping out from a secure and relatively safe environment of working in someone else’s laboratory and crossing the line to being the leader in my own laboratory.

I am excited about the chance to talk to other scientists and researchers about my ideas and how I think that I can contribute to the institutions that I will be applying to. I know there will be some moments over the next few months that this will seem a daunting task, but I am lucky to have good mentors and a great support group. Stay tuned to progress reports and I’ll see you on the other side.