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.

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.

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.

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.