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.

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.

Community

I am returning home from two exciting days at the National Science Foundations where I have been taking part of a funding proposal review panel. The review process is an integral part of how science is conducted in the United States and being asked to serve on a panel is considered a tremendous opportunity to give back to the scientific community. This was the first review panel that I have participated on and I was quite anxious about the whole experience.

I sat in the orientation meeting, towards the back, observing, taking in the experience. There room was about half full. As people kept coming in, I saw some of the older members recognize faces and walk over and shake hands or hugs. Introductions were made, names were exchanged, it was like a reunion of friends who had brought their own friends along to the gathering.

At that moment I had an epiphany of what the term scientific community means. It is not this cold, calculating set of individuals who sits and passes sentence on the veracity of a particular new finding or that drives the acceptance of a new hypothesis. It is just that, a community of individuals from all walks of life; breathing, walking, sharing, egotistical, humble …

This is where I feel at home. In the midst of this community; scientists.

An Anniversary to Remember

The Queen of Hearts
The Queen of Hearts

Three years ago at this moment I was sitting in a room in a hospital waiting.  Restlessly waiting, for the heart surgeon to stop by.  It was a beautiful cold and sunny day, just like today.  Christi was there.  She had flown in from New York City for a couple of days.  Mr. and Mrs. Burns were there. Mrs. Burns quietly reading, Mr. Burns checking his Blackberry, making sure every one was taken care of.  We were a bundle of nerves.

Lily had gone into surgery earlier that morning.  Open-heart surgery.  Not your normal lets change a valve or two surface scratching in your chest cavity brand of surgery you hear are so routinely done these days.  The doctor was going to stop her heart, cut into her heart, sow up a tiny little hole in the middle of her heart, and then close it all up in hopes to alleviate the cause of her recent stroke.

A little past 11 that morning, the doctor came in. He spoke with us and told us that the surgery had been a success. Just a short 8-10 minute operation. A routine task, for him, as he had developed this procedure. Lily would be in the ICU soon and we would be able to see her soon.

At half past noon, we were allowed to go see Lily. I still remember her laying there in the bed, with all those tubes in her. Later, as she awoke from the anesthesia, still groggy from the surgery and the pain drugs, she turned and smiled at me. I felt relief. The beginning of the road to recovery and physical healing for Lily and for us. The stroke that happened earlier that summer had been a life-changing incident. The open-heart surgery repaired that little hole, the culprit, of that devastating event. It did not stop us. We were moving on.

The last three years have been some of the best of my life. We still live with the aftermath of a stroke and open-heart surgery. This is now a part of our story. I am still amazed at her strength of will and at her courage. We were both lucky.  Living in Boston. Close to such great medical centers. An incredible support group of friends and family. But most of all, I am lucky for still having Lily in my life.  Thanks for all that you are and all you mean to me.  Besos.

If you want to know more about stroke and heart disease, please visit the American Heart Association web site. Please help stop the number 1 killer of moms, daughters, sisters, friends, and lovers in this country. Know the signs.