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 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.

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.