Data visualization helps engineers “see” more

As single-cell technologies continue to improve, it has become possible to measure multiple parameters simultaneously at the cellular- and even subcellular- level. Flow cytometry, for example, allows for the measurement of hundreds of properties for each cell, including features related to its shape, size, and protein expression levels. This new information has allowed for the discovery of behaviors that were previously unseen using population measures, such as Western blotting.

Example of data visualization (Source: http://www.flickr.com/photos/luc/5418037955/)

Example of data visualization (Source: http://www.flickr.com/photos/luc/5418037955/)

Along with this new information, however, comes a challenge. With multiple dimensions of data, it is difficult to perceive and properly interpret the message presented. Because of this, much of the information gained from single-cell resolution can be obscured or completely lost depending on the way the data are presented.

This perception problem leads to the need for dimension reduction, or a method that can transform the multi-dimensional data into a dataset with only two or three dimensions. To do this, a technique, “t-SNE”  was developed to visualize multi-dimensional data through the identifications of similar clusters within the dataset. t-SNE works by minimizing the differences between data points in order to identify the regions where data are most similar. Once these similarities are identified, t-SNE remaps the multi-dimensional data into three dimensions for visualization – two arbitrary axes and color, for visual separation of clusters. This remapping of the data allows for visual identification of the difference in data points that would be nearly impossible to show with the data in its original form.

One current application of t-SNE, a joint effort from groups in Stanford and Columbia University, uses this data visualization technique to show the heterogeneity in leukemia, and even the tumor subtypes they believe are responsible for relapse. This group took bone marrow samples from individuals who were considered healthy and those with leukemia, and compared these samples using flow cytometry.

With flow cytometry, they were able to study the expression of 29 different proteins, as well as the morphologic features of each cell. After processing the data using t-SNE, the group was able to not only distinguish the healthy cells from the cancerous cells, but also identify the protein expression profiles that were associated with relapse in these patients.

Data visualization is an increasingly important area of research as the amount of information gained from each experiment continues to increase. t-SNE is only one example of many that aims to allow for better perception of high dimension data to maximize its impact. This highlights the need for a researcher to not only design well-planned experiments, but also be creative with the presentation of their data. Creativity, combined with interesting data, will allow for a more thorough presentation of information and ultimately foster a better understanding of many areas in biologic research today, from genomic data to single-cell technologies.

Jacob Sarneki is a second year PhD student in Dr. Wirtz’s lab working on quantification of signal transduction at single cell resolution.

Info sessions on international research internships

IMEC clean room

What’s better than working on a cool research project in your lab? Why it’s working on a cool research project in a fascinating European country, of course!

Johns Hopkins Institute for NanoBioTechnology offers undergraduate and graduate research internships at IMEC’s world-class nanofabrication laboratory in Belgium. Internships last approximately 10 weeks and include housing and a stipend. Find out how to apply and what kinds of projects are being sought at one of our upcoming informational sessions. Two sessions will be held October 8, one at 1 p.m. with light refreshments and a second at 5 p.m. with pizza, both in Croft Hall, Room 170.

RSVP is required to Tom Fekete at tfekete1@jhu.edu

Lab coats are summer gear for high school researchers

You don’t think of a lab coat as summer wear for teens, but we don’t quite feel like it’s summer around here until our research interns have arrived. Early in June, INBT’s undergraduate nano-bio researchers arrived. This week our high schoolers in the Summer Academic Research Experience (SARE) scholars got started.

SARE pairs specially selected teens with university mentors who guide them through a mini research project. At the end of their time here, they hold a small poster session. The students gain valuable work skills, learn about scientific careers, get tutoring help, practice their writing, gather data for their projects and earn some cash for the future. Students in the program are recruited from the Boys Hope Girls Home of Baltimore program, The SEED School of Maryland and The Crossroads School, all of which assist in differing ways with in the education, housing, tutoring  and counseling of promising young people from disadvantaged circumstances.

The SARE program was launched in 2009 by Doug Robinson, professor in the cell biology department at the School of Medicine, and is funded jointly by the medical school and Johns Hopkins Institute for NanoBioTechnology.

This year’s SARE scholars include: Diana Bobb is being mentored by Makoto Tanigawa in the Takanari Inoue Lab in the Department of Cell Biology; Kaleel Byrd is being mentored by Ryan Vierling in the Caren Meyers Lab in the Department of Pharmacology; Milan Dower is being mentored by Tom Lampert in the Peter Devreotes Lab in the Department of Cell Biology; Jewel Herndon is being mentored by Herschel Wade in his lab in the Department of Biophysics; De’Sean Markley is being mentored by Hoku West-Foyle in the Douglas Robinson Lab in the Department of Cell Biology

High schoolers to show off their summer research

Stephanie Keyaka (left) working with Jincy Abraham (Notre Dame) in the Craig Montell Lab. Photo by Mary Spiro.

The Summer Academic Research Experience (SARE) pairs specially selected teens who come from academically disadvantaged homes with university mentors who guide them through a mini research project. The students gain valuable work skills, learn about scientific careers, get tutoring help, practice their writing, gather data for their projects and earn some cash for the future. The group will present their research findings during a poster session at the Johns Hopkins University medical campus on August 20 in the Bodian Room (1830 Building Rm 2-200) from 3:30 to 4:30 p.m.

“This is way better than flipping burgers,” laughed Stephanie Keyaka, as she prepared an image of a Western Blot performed on  Drosophila (fly) eye genes.

Keyaka is one of three high school students who worked in a biological chemistry laboratory  this summer with financial support from Johns Hopkins University Institute for NanoBioTechnology and School of Medicine.

Christopher Miller (right) with his mentor Hoku West-Foyle. Photo by Mary Spiro.

Keyaka, a rising 10th grader from The SEED School of Maryland, will be joined at the poster session by Christopher Miller, also a rising 10th grader from The SEED School of Maryland and Shaolin Holloman, a rising 11th grader at Baltimore Polytechnic Institute who is part of the Boys Hope Girls Hope of Baltimore.

The SEED School of Maryland is a public boarding school that accepts qualified children from across the state entering the 6th grade.  Boys Hope Girls Hope is a privately funded nonprofit that offers students the chance to attend academically challenging public or private schools and the opportunity to live in the Boys Hope or Girls Hope home.

Miller studied the protein myosin in the cell biology laboratory of  associate professor Douglas Robinson. Holloman worked in the cell biology lab of professor Carolyn Machamer on a project that sought to understand why the SARS coronavirus localized in the Golgi apparatus of the cell. Keyaka studied rhodopsin in the eyes of flies the lab of professor Craig Montell.

Shaolin Holloman (left) with professor Carolyn Machamer. Photo by Mary Spiro.

Help celebrate the accomplishments of our summer high school students who participated in the Summer Academic Research Experience. This event is free and open to the entire Hopkins  community. Light refreshments will be served. Students, faculty and mentors will available to discus the projects.

 

 

 

Money makes the (research) world go ‘round

Photo Illustration by Mary Spiro.

Grant money drives research, but obtaining funding can be a daunting task for those unfamiliar with the process. Wouldn’t it be nice to have someone to show you the ropes?

That’s why three postdoctoral fellows from Johns Hopkins Institute for NanoBioTechnology were asked to present a sort of crash course in how to get those almighty research dollars. The talk, given as one of INBT’s professional development seminars on July 27 to a group of graduate, undergraduate and a few high school summer research interns, covered basics, as well as some commonly overlooked issues encountered in the grant application process.

“When applying for grant funds you have to assume that everyone else also has a good idea. Your idea has to be better than great; it has to be outstanding,” Eric Balzer told attendees. Balzer is a postdoctoral fellow with professor Konstantinos Konstantopoulos in the department of Chemical and Biomolecular Engineering.

He also advised the group to avoid novice grant writing errors such as “submitting a proposal on lung cancer to an agency that only funds breast cancer research.” In other words, read the funding agency’s mission statement.

Yanique Rattigan stressed the importance of avoiding overly complex language in grant applications. “Grant reviewers often include patient representatives who are not scientists and engineers, so you have to make sure that there is a section describing the research in lay terms that they can understand,” offered Rattigan, who is conducting research in the pathology lab of professor Anirban Maitra at the Johns Hopkins School of Medicine.

Granting agencies look to fund novel research ideas, explained Daniele Gilkes. “They want to know how your work will fill in the knowledge gaps that exist in the field. You can determine this through thorough analysis of the current literature pertinent to your area of research,” added Gilkes, who works with Denis Wirtz, the Smoot Professor of Engineering in the Department of Chemical and Bimolecular Engineering.”

The group stressed the need to edit and re-edit a grant application prior to submission, and emphasized the importance of choosing the right referee to compose letters that truly support the candidates potential for independent research.

The teams’ insight into the grant application process can be found in this SlideShare slide show, click here.

Story by Mary Spiro.