Kaushik Gopu joined the team

UNC Charlotte Computer Science graduate student Kaushik Gopu joined the IGB application development team in May of 2023.

Since joining the team, he has been working on adding new features to Integrated Genome Browser and on updating the IGB App called ProtAnnot. He also has contributed to improving our use of OSGi frameworks, by trying out and reviewing various on-line tutorials discussing declarative services annotations and their use.

In only a month, you’ve contributed a lot. Keep up the good work!

The Last Scientist for a Day of the 2015-2016 School Year

This month, we introduced high school students to the field of personal genomics. Ivory, April, and I taught kids how to analyze genetic variation data from 23&Me using Integrated Genome Browser. Ann attended and worked through the exercises along with the kids.

This week, we showed 4th graders how we grow plants in the lab.

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I explained that one of the biggest reasons we study plants is to develop hardier, more nutritious crops. I showed them Arabidopsis plants and introduced the concept of a “model” organism in research. Arabidopsis plants are tiny and grow quickly – like weeds – which makes them ideal for quickly testing theories about how plants grow.

Then, they got their hands dirty transplanting radish seedlings from petri dishes into soil – just like we do with Arabidopsis seedlings when we want uniform growth.

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Everyone in the Loraine Lab had a lot of fun helping out with the Scientist for a Day program. I’m sure we all learned as much from the experience as the students. We all look forward to showing of our research to more Kannapolis students next school year.

18th Annual Plant Genome Awardee Meeting

On the first of September I began my National Science Foundation postdoctoral fellowship through the plant genome research program. As such, I was able to attend this year’s Plant Genome Awardee Meeting along with Dr. Loraine. It was a great opportunity to hear talks on the latest plant research and exchange ideas with other plant geneticists. I had a great time, and am looking forward to next year’s meeting.

There were two days of talks on the latest research into plants.

There were two days of talks on the latest research into plant genetics and biology.

2015 Plant Biology Meeting

The Loraine lab traveled to the Minneapolis convention center for the 2015 American Society for Plant Biology meeting. There were many great talks given on recent advances in plant biology and crop sciences. Our own April Estrada gave a talk on the role of the gene SR45a in stress response in plants. I gave a talk on using IGB as a resource for teaching, as well as a workshop introducing visual analysis of RNA-seq data.

April giving her talk on SR45a

April giving her talk on SR45a

Everyone had a great time at the various talks, workshops, and exhibits. It was also a great chance to network with other researchers. Of course, we also made sure to take some time to visit the Twin Cities.

Enjoying Minneapolis

Enjoying Minneapolis

2015 Society for Developmental Biology

I want to thank the Society for Developmental Biology for inviting me to their annual meeting in Snowbird, Utah. I had the opportunity to give a talk on the work that April Estrada and I have done on the role of SR45a in alternative splicing in stress response. I also led a workshop on using Integrated Genome Browser to visually analyze high-throughput sequence data. We had a great turnout, as many of the attendees were very interested in using IGB in their work.


SDB attendees finding out more about IGB.

Snowbird is a ski resort located in the mountains near Salt Lake City. I was able to take the tram to the top of the mountain and take some photos. It was a great location for a conference.


View from top of Snowbird, looking out over Salt Lake City.


How to take notes on a bioinformatics project

Notes on data processing should follow these guidelines:
  • Each entry starts with the date in bold.
  • Each entry is a bulleted list.
  • Bullets should be clear but they do not need to be complete sentences, and people can be referred to by initials for brevity.

Include information about what was done and where to find the results, but do not clutter this document with why anything or how exactly; that information belongs elsewhere.

Information to include
  • Links (or paths) to data, reports, web resources, more detailed summaries, etc.
  • Basic description of what files are made and where to find them.
  • The line of code used to run a process
  • The fact that a process completed successfully or notes about what indicated that it did not.

Information to include elsewhere,
(put a link the in the data processing notes, don’t write it out here)

  • Rational about why the parameters used were chosen.
  • Experiment layout, background, reasoning, results, discussion.
  • Explanations about why a process did not work, and why the fix does.

4th Annual Catalyst Symposium

The Loraine lab had a strong showing at the 4th annual Catalyst Symposium, with Ivory, April, and I presenting posters on our current research.

The title of the symposium was “Progress in NCRC”. The theme was to highlight the highly diverse and interdisciplinary research being conducted across the North Carolina Research Campus. There were nine talks, eighteen posters, and over a hundred attendees. The talks and posters were very good, covering topics such as the role of obesity in promoting cancer and finding what genes control the taste of fruits and vegetables.

Ivory and April presented posters on their work in rice and Arabidopsis, respectively, while I presented the latest features in IGB. It was a lot of work to prepare for the symposium, but everyone had a great time and learned a lot.


Farewell Tarun

Yesterday we had a lab dinner to celebrate Tarun Kanaparthi’s December 2014 graduation – he is earning his Masters degree in Computer Science from UNC Charlotte.

Following a vacation, he plans to start work at his new job, to be determined. Like many recent or soon-to-be graduates in computer science and bioinformatics, he is trying to decide between multiple opportunities. It’s nice to know that computer programming and data analysis skills are still in demand. Congratulations Tarun!

Here is a photo from the going-away party. From left to right, we are:

April Estrada, Ivory Blakley, Mason Meyer, David Norris, Tarun Kanaparthi, Tarun Mall, Nowlan Freese