The Loraine Lab would like to welcome Jessi Davis to the group. Jessi was selected through the 2016 Research Campus Plant-Bio Summer Internship program. She joins us from AL Brown High School, where she will begin her senior year this fall. Jessi will be spending her summer working on designing artificial microRNA to knock down expression of genes in Arabidopsis thaliana.
Now that IGB 9 is out the door and into the hands of users, the team and I are focusing our full attention on developing our all-new genome browser – IGB-fx.
We’re calling it IGB-fx because it uses JavaFX, the graphics toolkit that is replacing Swing in the world of Java-based user interfaces. But that’s only a small part of what makes it much better. The main innovation is that IGB-fx – built from the ground up – is 100% services based and modular. Yes, we are finally all-in for OSGi. IGB 9 and earlier versions were also services based, but there were too many interconnected classes and packages. Making changes to the code required understanding too much of it, which made adding new features too difficult. Since we are an academic, open source project in a rapidly changing field, we need a code base that exemplifies good engineering practices and is easy to modify. In other words, we need a strong foundation on a large lot with room to expand.
Recently, I wrote a quick start guide to building and running IGB-fx. Here, I’m going to describe the steps in more detail and also explain how to load data into the browser. I’ll also explain how to use our fork-and-branch workflow.
To get started, you need git, Apache maven, karafe, and Java 8. We use git for version control, maven (mvn) to compile IGB-fx, and the karafe OSGi container to run it. IGB-fx needs Java 8 because it uses lots of features new to Java 8, like lambdas.
To develop IGB-fx:
- Go to Bitbucket.org and sign up for a free account.
- Go to the IGB-fx team repository and fork the repository. Here’s how: On the IGB-fx team repository home page, click the Actions button (three dots, top left) and choose Fork. This makes a new IGB-fx fork belonging to your user id.
- Go to the Web page for your new fork on Bitbucket. Copy the git URL in the upper left.
- On your local computer, clone the project.
- After cloning the project, add the team repository as a new remote repository. You can name it whatever you like, but to be consistent with other projects, name it “upstream” like this:
git remote add upstream https://bitbucket.org/lorainelab/igb-fx
Now, you’re ready to build and run IGB-fx:
- Open a terminal window and change into your cloned fork.
- Build the project using maven.
- Start the karaf shell and use it to run IGB using the provided start-shell.sh script.
Commands to do the above are:
mvn clean install start-shell.sh
Get some data and load it
If you have a fast internet connection, the fastest way to start viewing data in IGB is to open the human genome. Inside IGB-fx Current Genome tab, species Homo sapiens and genome version H_sapiens_Dec_2013 from the two menus. Gene models will load automatically. To load sequence, click the Load Sequence button. This will trigger downloading of a compressed copy of the human genome sequence. This works best on a faster internet connection.
If your internet connection is slow (10 Mbs or less), open a much smaller genome. The fruit fly or Arabidopsis genomes are about ten times smaller than the human genome, and so that are a good choice.
To get the fruit fly genome sequence and gene models annotations:
- Make a folder on your computer where you will keep these files long-term. If you move them, the IGB-fx prototype won’t be able to find them again.
- Go to the IGB Quickload site folder for the 2014 fruit fly genome.
- Download three files and move them into your local folder. The files are:
- In IGB-fx, select File > Open Custom Genome.
- Under Reference, choose the compressed sequence “2bit” file.
- Under Genome Version, type “D_melanogaster_July_2014″
- Under Species, type “Drosophila melanogster”
- Open the annotations file. In IGB-fx, select File > Load File. Select the compressed, indexed gene model file: D_melanogaster_Jul_2014.bed.gz. Note: you may have to uncompress it first.
- In IGB-fx, click “Load Data” to load gene models. Click “Load sequence” to load sequence data. To zoom in and see the sequence, click-drag over the number link or drag the slider to the right. Pan from side to side using the panning scrollers at the bottom of the display.
Students and collaborators developing IGB-fx should use the fork-and-branch workflow. This blog post does a great job of explaining it and Atlassian also provides excellent documentation. In a nutshell, when you start work on a new feature or bug fix:
- On your local computer, create a new branch.
- Make changes. Add and commit changes to your local clone.
- Push the changes to your fork on bitbucket.
- On the bitbucket page for your fork, create a pull request. The source should be your branch and the target should be the master branch of the team repository. (Recall you added the team repository as a remote called “upstream.”)
- Wait for review. Use the review feedback (if any) to correct problems or make improvements. Note that any new changes you push to your fork hosted on bitbucket will automatically get added to your pull request.
Once your pull request gets merged into the master branch, you should update your fork:
- In your local clone, switch to the master branch.
- Pull master branch changes – including your pull request – from the team repository, nicknamed “upstream”
- Merge these changes into your local clone.
- Push them to your fork to update it.
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.
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.
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.
Update – July 29, 2016
Due to scheduling and technical issues, we will offer BINF 3201 and BINF 3201L in spring 2017 instead of fall 2016.
We plan to make the Spring offering better than ever, featuring new content and introducing new sequencing methods and applications. Therefore we highly recommend reserving time in your schedule to take the the class in Spring of 2017. Check back here for more information or feel free to get in touch!
The Bioinformatics Department at UNC Charlotte has developed a great class for students from CS, SIS, Biology and Bioinformatics to get hands-on experience in genomic methods, focusing on DNA sequencing.
These days, nearly everyone in biology uses high throughput sequencing methods in research. And these methods are getting cheaper, faster, and more accessible. Very soon – possibly within only a few years – you’ll be able to get your own personal genome sequenced. If you’re considering a career in medicine or biotechnology, you need to understand how these methods work.
However, many people who use sequencing methods don’t know much about them. We don’t sequence our DNA directly – first we extract it and convert it into a library. How we make these libraries dictates what we can do with the data later. In this class, you’ll gain in-depth, first-hand knowledge of how we convert DNA into libraries into data.
You’ll learn how to create a sequencing library from genomic DNA using a technique called long-range PCR, the same method you could use to sequence select human genes. You’ll sequence the library using an Ion Torrent Personal Genome Machine (PGM), a low-cost sequencing instrument ideal for learning the basics. In the process, you’ll also master basic molecular biology techniques – like how to pipette, how to extract DNA from a sample, how to run a gel, and how to design and perform a PCR experiment. By the end of the semester, you should be well qualified to start an internship in a molecular biology laboratory – or apply to a Ph.D. or health professions program to continue your training.
Outside of lab, you’ll learn about many different approaches to sequencing, such as the limitations and strengths of different sequencing platforms. You’ll also learn to use software tools to visualize and interact with data, such as Integrated Genome Browser, developed here at UNC Charlotte. And then you’ll apply what you’ve learned by writing a mock grant application proposing an experiment that uses sequencing to answer a research question. (We’ll provide plenty of ideas to help you get started.) Last but not least, you’ll give a presentation on your idea.
Undergraduate level BIOL 1110 Minimum Grade of D and Undergraduate level BIOL 1110L Minimum Grade of D or Undergraduate level BIOL 2120 Minimum Grade of D and Undergraduate level BINF 1101 Minimum Grade of D
Congratulations to Tanner Deal for tying for first place in UNC Charlotte’s microscopy competition: Visualizing Science. His image “Oryza” is of a developing grain of rice he collected from his experiments. To read the full description, as well as see all of the other microscopy images, check out the online exhibit – https://library.uncc.edu/exhibit_upload/
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.
We’re excited that Tanner Deal has decided to stay in the Loraine Lab through the next year. Tanner did an excellent job throughout his summer internship, conducting experiments in molecular biology and taking care of the various plants being grown in the lab.
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.
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.
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.
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.
The Loraine lab would like to extend a warm welcome to Tanner Deal. Tanner joins us from A.L. Brown High School, where he is an incoming senior. Throughout the summer, he will have the opportunity to explore plant biology, molecular research, and learning about genomics software. We’re all excited to have Tanner as part of the team.