Measuring the Success of a SAMSI Program – My Experience at the Beyond BIoinformatics Transition Workshop

The following was written by Katerina Kechris, Associate Professor and Graduate Program Director, University of Colorado – Denver. School of Public Health.

Katerina Kechris

Katerina Kechris

In mid-May 2015, working groups from the Beyond Bioinformatics Program gathered during the Bioinformatics Transition Workshop. This was a culmination of eight months of progress for over 10 working groups. The workshop topics were diverse and covered a variety of topics including epigenetics, microbial communities, evolutionary models, imaging genetics, next generation sequencing errors, high-dimensional discrete data, multiple hypothesis testing and data integration. The diversity of these topics reflects the current state of research in the biomedical sciences where technologies are advancing the study of biological mechanisms, structures, populations and disease. These technologies are generating high-dimensional and complex data structures providing intriguing opportunities for statisticians, mathematicians and computer scientists to develop new models, methods and algorithms to answer important biological questions.

Group photo outside

The Beyond Bioinformatics Transition Workshop attendees.

As a leader for one of the two Data Integration working groups, I was excited to hear about the activities from the other working groups during the workshop. I found their progress impressive, considering that many of the group members did not know each other until the Opening Workshop just eight months earlier. The transition workshop gave me the opportunity to reflect: How does one measure success of a program year and a working group? There are the usual metrics of publications, conference presentations and grant proposals that will be documented in great detail for reports. But at the workshop I could see more qualitative and interpersonal measures of successes. First, new collaborations were developed among researchers who would otherwise not have had the opportunity to meet and work together.

Personally, I enjoyed getting to know and working as a team with the other Data Integration working group leaders and members. Second, I was pleased to see great attendance and presentations at the workshop by students and post-docs. I know in several cases that the working group facilitated thesis and post-doctoral research projects for these junior investigators. Finally, I observed that there are ongoing plans to continue the working group efforts beyond the formal program year, which speaks to the positive aspects of the program. As for our working groups, it was such a pleasure to make new colleagues and see the evolution of how we approached the problem of data integration with very different perspectives and methods. I look forward to learning about the continuing progress of all groups.

Classroom shot of people listening to lecture

Listening to a working group make its report.

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Recovering from the Epigenetics Workshop

three people talking at the meeting

Michael Zhang (UT Dallas), Zhaohui (Steve) Qin and Shili Lin (Ohio State, co-organizer)

The following is from Zhaohui (Steve) Qin, Associate Professor, Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, who attended the SAMSI Epigenetics Workshop March 9-11, 2015.

I was sitting near my departure gate at RDU Wednesday afternoon, waiting for my return flight after attending the SAMSI workshop on Epigenetics. Suddenly I feel so tired. I have good reason for being exhausted. I feel that my brain has been set on high-spin mode all of the last three days. This is so strange. It is supposed to be a low-intensity meeting. Only a handful of talks and just about 50 attendees. It feels so different from attending other conferences such as ENAR, JSM or ASHG.

First, I know almost everyone at the workshop. For the speakers, I either know them personally, or I know their work. At every break, I barely have time to grab a cup of coffee, not mentioning checking emails. There is always someone I want to talk to within five feet of me wherever I go. And not like the massive conferences, there is plenty of space at the corridor in this cozy SAMSI building. So I feel totally comfortable to join in a conversation.

Inkyung Jung (UCSD), Chenchen Zou (Jackson Lab) and Miriam Huntley (Harvard).

Inkyung Jung (UCSD), Chenchen Zou (Jackson Lab) and Miriam Huntley (Harvard).

Second, there is so much to learn, to talk about and to think. Epigenetics is a hot area these days, new technologies and new findings are emerging almost daily. This is a great opportunity to immerse myself in this exciting field, with so many experts in these areas walking around me. Thanks to Dr. Shili Lin, the set of speakers at the workshop is amazing. A few senior and very experienced scientists plus a large cohort of young and energetic young scientists. In the past three days, I learned several new ideas or results/findings. And I am pretty sure my fellow attendees felt the same way. Everyone is asking each other what’s new. I won’t be surprised if new collaborations were started right at the workshop. I wish more conferences I am going to will be like this one. And I am certain that I will come back to this nice little building when the next opportunity arrives.

Group of people sitting looking at laptops during a break

Yongseok Park (U Pittsburgh), Inkyung Jung (UCSD)

I felt so sympathetic towards my colleagues Karen Conneely and Hao Wu, who have to drive six hours back home. How can someone still have the energy to do that after three long days is really beyond me. I am determined that I am going to sleep soundly during my flight back, no matter how bad the turbulence is.

And I did.

SAMSI-SAVI Workshop on Statistical Methods for Bioinformatics: December 2013

The following was written by Malay Bhattacharyya, Department of C.S.E., University of Kalyani, India

Malay Bhattacharyya

Malay Bhattacharyya

“Don’t give a talk, take a class.” This was the driving force, as I feel, behind the SAMSI Workshop on Statistical Methods for Bioinformatics we had at the IISc campus, India during Dec 12-14, 2013. It included people from diverse backgrounds encompassing biologists, statisticians, mathematicians, computer scientists, biostatisticians, biophysicians, biochemists, anthropologists, and lot more.

The Department of Mathematics at IISc was a perfect inspiring venue for this workshop, particularly for research discussions. It has chalks and boards kept everywhere, at every corner of the department! Even I saw a catering person to write random equations (although trivial) on a board avoiding others’ notice. Environment really motivates!

The very first talk of the workshop, by Varghese George of Georgia Regents University, made us feel like entering into the revitalized world of the epigenetics. The recent progresses and futuristic goals were very nicely introduced. Both Indranil Mukhopadhyay of ISI Kolkata and S. R. Deshmukh of University of Pune had comprehensive introductory talks afterwards about the basics of statistical tests, molecular biology, etc. and about expression profiling, respectively. Many of the speakers were also benefited from their efforts of making a strong foundation of the preliminary concepts. It was not required for them to start from the scratch.

The first day was so windy that I felt possibly the air is also keen to enter into the lecture hall, a perfect learning platform! What I liked most is not only the respective speakers were responding to the questions, rather everybody took the pain to discuss and settle the best answer for the tricky ones. The sessions were not too much attendee-heavy, so everybody had a fair chance of asking questions. Again, the ratio close to 2:3 between the invited speakers and the participants set up a real platform of face-to-face learning.

Naomi Altman of Pennsylvania State University gave an attractive talk on the recent obesity of the high throughput data. The reproducibility of research became a major issue of discussion lead by the talk of Prof. Altman. It is really a burning issue worldwide. There was a common agreement between all the invited speakers, who strongly encouraged keeping the relevant source codes also available alongside the publications.

How statistical analysis can help in some particular areas of plant genetics, especially in the gene duplication problems, was thoroughly described by the SAMSI Deputy Director Snehlata Huzurbazar. It was also a real pleasure to have Ashis Sen Gupta of ISI Kolkata on stage to talk about his work on understanding the circadian rhythms. It is a real challenge to build statistical models given the surprising fact that “the rhythm of the life is circular, although the life is itself a linear game.”

The next day we also had a great experience! Everybody was cracking jokes with the “Friday the 13th” issue that eventually marked out the second day of the workshop. But it was really an enjoyable day – not only for the banquet but also for the diversity and depth of the talks. It started with the talk by Nagasuma R. Chandra from the host institute who gave a realistic overview of how to proceed step-by-step towards the modelling of disease prediction. She has a strong belief that making such systems automated will indeed speed up the progresses in this direction.

Olga Vitek from Purdue University gave us an all-inclusive glance toward the immense scope lying in some promising areas of proteomics. Again, N. Srinivasan of IISc detailed on a fantastic account of his research on finding missing links between protein families using computational models.

T. S. Vasulu of ISI Kolkata and Paul Joyce (I love the way he explains complex things with funny examples) of University of Idaho gave nice introductions to statistical methods that can be applied to phylogenetic analysis and for the study of adaptive evolution, respectively. Switching between the laser pointer and the hard pointing stick was a real fun for Prof. Joyce.

India-GroupShot

Every talk was made somewhat flexible based on the demand of the attendees. I remember a talk to have been stretched by half an hour or so to satisfactorily answer every question raised by the listeners. Still the overall time frame for the entire day was well maintained. We also had a nice photo session on the terrace of the hosting department in a mood of get together.

The long walks (voluntarily avoiding cars) through the woods of the campus of IISc with many of the speakers, while returning after the workshop days, gave me pleasant chance of gaining additional experience through informal discussions. Research is no more an independent effort, rather a collaborative competition.

The final day of the workshop started with a nice talk by Susan Holmes of Stanford University, who highlighted diverse facets of the Human Microbiome Project. Her idea of more on leaps less on slides was great, using the chalks and boards every time. The concluding talk by Sanghamitra Bandyopadyay of ISI Kolkata, a very basic one bridging between statistics, computer science and biology, detailed on various robust computational models that can tackle multi-objective problems, often occurring in expression analysis and related areas.

The contributory talks by seven of us, mostly covering ongoing studies, were strongly benefitted from the expert speakers being also a part of the audience. I enjoyed my contributed talk and received a couple of valuable suggestions. The take home message was “do whatever you wish to do, but with a clear conception and full confidence.” We were unfortunate this time to miss the talk of K. Thangaraj of CCMB, on the very last day because of his absence due to some urgent involvements.

I hope that the slides of the talks will soon be available online. The logistics managed by Shruti and Sai were fabulous. The foods were so diverse that I experienced the taste of the entire India. The organizers took a lot of pain to arrange a great banquet dinner on the second day. The round table discussions in the banquet session were really effective.

I feel like SAMSI workshop proved to be a real SAMSI (such a mega statistical incident). Hats off SAMSI!