Neat Science Thursday – Scientific communication is hard

For my dissertation research, I studied the mechanisms of viral persistence in the central nervous system using an in vitro model consisting of picornavirus infections of differentiated and undifferentiated murine neural progenitor and stem cells.

To some of my non-science friends and family, that explanation sounds something like, “I studied blah blah blah, miscellaneous pretentious scientific jargon, blah blah.”

Of course, they would still have no idea what I studied, and any further attempts to explain would be met with that kind, patient look that people give you when they’re bored but are too polite to walk away.

So I would tell non-science people that I studied “how a virus hides in the brain for a long time, and the consequences of having a virus hiding in the brain using mouse stem cells”.

This explanation will elicit much more interest, but can sometimes get distorted when described second-hand to others since it’s not as accurate. Also, there may be some fellow scientists who will think you lack professionalism, or don’t know what you’re talking about if you use this sort of description.

If you think about it, there is so much jargon specific to each field of study, it’s actually pretty impressive how well scientists have been able share information across disciplines. Of course, there is always room for improvement in that arena, especially since researchers primarily disseminate their findings via scholarly articles, keying them for easy search amongst fellow researchers in their discipline. The differences in jargon sets contributes to the difficulty in finding research articles outside your field of research which contain research findings that could have important impacts in your own work. It’s also why there has been a lot of interest in annotating research literature and making it more searchable (Go! Go! Mark2Cure) as well as creating an open database where information contained in research literature can be formally structured around a set of shared ontologies (Go! Go! Wikidata.

It’s also great that these findings are becoming more available as funding agencies help to drive open access policies enabling the public to finally access the research paid by tax/donation dollars. But open access does not mean accessible if we consider the sheer volume of jargon that must be learned in order to read and understand scholarly articles. How can we expect tax payers to support research if they are locked out on so many levels? Now before you argue that ‘people need to take personal responsibility for their own education’ or ‘the articles aren’t really hard to read if you actually put in the effort,’ ask yourself this, ‘Am I dismissive of people science communicators that communicate science via non-traditional channels (ie- non-academic journals)?’ If your answer is ‘yes’, you waive all rights to complain about the scarcity of research funding.

If your answer is ‘no’, consider contributing your expertise to a truly accessible knowledge-base/medium like Wikipedia. Efforts are already under way to make information on every human gene of interest publicly available on Wikipedia (the Gene Wiki initiative), and greater participation is needed from scientific community.

For those of you, researchers or not, who ARE able to communicate science with such elegance, enthusiasm, poignancy, and precision–especially those of you on non-traditional channels like Science 2.0, twitter, etc.–thank you for using your talents to engage the public so they can see how their money is being spent. You are awesome! The rest of us will just have to keep trying.

Surrounded by geniuses- part 11 : Erick

The new genius who was here before, but not was not mentioned when I first joined the lab because this genius was not (as far as I knew) actually a part of the lab…yet. Sure, his name floated around in the Su Lab chat channels, but he was not physcially present presumably because he was in another lab. I also saw him during some of the Su Lab meetings, but then again, there are also other labs which show up during these meetings, so his status was still unclear to me. What is clear is that the new genius who was here before, but not is a genius. Not only did he give a fascinating presentation on one of his research projects, he also has an MHS in Public Health AND an MD, which makes the new genius who was here before, but not the perfect person to conduct research on developing open source translational bioinformatics methods to advance personalized medicine.

Specifically, Erick’s research projects include:

  • Developing statistical methods for adaptive enrichment in clinical trials with extensions to post-hoc subgroup analyses.
  • Analyzing phased whole genome sequence data from the Wellderly Study
  • Developing computational tools for a massively-multiplexed and inexpensive gene expression assay (Rnl2-based RASLseq)
The new-genius-who-was-here-before-me-but-not has some impressive credentials
The new-genius-who-was-here-before-me-but-not is an expert in a lot of subjects, including PSB participation

Additionally, the new genius who was here before, but not is a pro when it comes to the Pacific Symposium for Biocomputing (PSB) and has dispensed great advice to the genius-in-charge with insane mental organizational skills on how to best enjoy the conference.

On a side note: In case you missed it, the genius-in-charge with insane mental organizational skills and the Young-dad-in-charge-of-too-many-crazy-projects genius along with some others will be helping to chair the session on crowdsourcing and data mining at PSB. Though it’s too late to submit a manuscript on this session topic, it isn’t too late to register for the conference.

Surrounded by geniuses- part 10 : Sal

Sal the professional...the professional integrated systems biology researcher
Sal the professional…the professional integrated systems biology researcher

It’s easy to get the wrong impression of the Tough-looking, badass genius, and much harder to accurately portray him. Sure, the Tough-looking, badass genius bears an uncanny resemblence to Leon (the titular character from Leon, the Professional), which contributes to this impression, but partially because he objects strongly to being called a genius. See, the Tough-looking, badass genius, Salvatore Loguercio, worked really hard to become accomplished in his field, so he would prefer that the term genius be reserved for people like Maryam Mirzakhani, the indisputable intellectual who won a prestigious Fields Medal this year. No one disagrees that Maryam Mirzakhani’s brilliance is on a completely different level, but this post isn’t about Maryam Mirzakhani. It’s about Sal.

Maryam Mirzakhani
No one disputes the awesomeness that is Maryam Mirzakhani.

Sal’s journey into the Su lab began even before he realized it. He originally began working on a dataset generated by the genius-in-charge with insane mental organizational skills back when the genius-in-charge with insane mental organizational skills was still at GNF. The two finally met at the 2009 ISMB conference. While still a Research Associate at the Biotechnology Center of the Technische Universität Dresden (BIOTEC-TU) in Dresden, Germany, Sal began collaborating with the genius-in-charge with insane mental organizational skills on semantic web integration in Gene Wiki plus in 2010. They met again in 2010 at the ISMB conference, and the genius-in-charge with insane mental organizational skills searched exhaustively for ways to officially bring Sal into his team. Unfortunately, the hurdles to do so were high and could not be cleared until the genius-in-charge with insane mental organizational skills moved from GNF to The Scripps Research Institute. After moving, the genius-in-charge with insane mental organizational skills contacted Sal in September of 2011, and officially brought him into the Su Lab in January of 2012.

At first, Sal worked on games with a purpose. In particular, he helped develop Dizeez and GenESP and contributed to the data analysis of The Cure. Towards the end of the year, Sal began moving towards analysis, integration, and modeling of data from collaborators (Dr. Ann Feeney at TSRI) to generate new hypotheses which could then be tested by the Feeney group. Simultaneously, he collaborated with Dr. William E Balch and developed the Network-Augmented Genomic Analysis (NAGA) methodology to integrate and utilize two somewhat disparate datasets generated by the Balch lab: 1. RNAi functional screening data, and 2. protein interaction data from mass spectrometry. Sal’s work on NAGA enables researchers to discover and prioritize pathway proteins and is currently being applied in at least five different labs.

In addition to working hard at multiple projects, Sal has not neglected the importance of networking and attributes much of his success to the mentorship and networking opportunities provided by the San Diego Center for Systems Biology. As a testament to his productivity, Sal was awarded a fellowship from the Cystic Fibrosis Foundation in 2013, and a seed grant from the San Diego Center for Systems Biology. Don’t be fooled by his resemblance to Jean Reno, the Tough-looking, badass genius is pleasant, good-humored, and serious about doing great research.

Surrounded by geniuses- part 9 : Louis

Be ready for anything when working on thrilling research
Be ready for anything when working on thrilling research
Trail-mix-and-red-bull genius is a Graduate Student in the Kellogg School of Science and Technology at The Scripps Research Institute, which explains his ability to live off standard graduate student fare like Red Bull and trailmix. The Trail-mix-and-red-bull genius, Louis Gioia (pronounced loo-is joy-ah), joined the Su lab in January of 2014 during the great influx of 2014 (note- the year is not over yet, so it’s not too late join the deluge of new members). Since he joined the lab, the Trail-mix-and-red-bull genius has been strengthening his computational and analytical acumen by riding what can only be described as the roller-coaster of research programming, which looks something like this:
The research programming roller-coaster
The research programming roller-coaster

In Louis’s case, he began working on snp annotations for the OncoRep project when he first joined as a rotation student, and then transitioned into working diligently on the Omics pipe project as he became an official member of the lab. As the Omics pipe project nears completion, the Trail-mix-and-red-bull genius has recently joined a new project on the meta transcriptomics of the microbiome (so you can imagine the ride he has ahead of him.)

Surrounded by geniuses- part 8 : Vyshakh

Around the time I joined the lab, a Fellow-new-person-but-smarter genius also joined as a summer intern. The Fellow-new-person-but-smarter genius, was once a Software engineer for Infosys Technologies Ltd where he developed the Java/J2EE based E-Commerce website Spring and Hibernate Web Application framework which included
• Designing proof of concept (PoC) for Warehouse Inventory Management using Sterling IBM Ecommerce Development tool for Distributed Order Management
• Working on Localization and Internationalization module for the website
• Integrating and testing Sterling OMS with Oracle SQL and JSP using Java, Hibernate and Spring MVC framework

The Fellow-new-person-but-smarter genius, Vyshakh Babji joined the Master’s program in Computer Science at San Diego State University and has taken part in several successful projects.

As part of the Su Lab, Vyshakh is working on an outgrowth of The Cure: Branch. The Cure was a challenging game which allowed players to help scientists to select genes for predicting breast cancer survival. See the recently released paper on The Cure here. As a game, The Cure was a quite challenging for players with no expertise in the field of breast cancer, but could be very powerful in the hands of experts. Why not give experts biologists more control in the process of selecting and organizing genes and their associated disease outcomes? Thus was the idea for Branch born, and researchers at the Su Lab like the Fellow-new-person-but-smarter genius, the Insanely-talented-undergrad-genius, and the Young-dad-in-charge-of-too-many-crazy-projects genius have been hard at work building Branch. As a tool, Branch will enable expert biologists to easily engage directly with high-throughput datasets without the need for a team of bioinformaticians. Using a tree building process, Branch allows researchers to rapidly test hypotheses about interactions between biological variables and phenotypes in ways that would otherwise require extensive computational sophistication. In so doing, this tool can both inform biological research and help to produce more accurate, more meaningful classifiers.

Contributing the development of Branch, Vyshakh has:
• Been involved in writing Application work flow both for front end and backend.
• Supported the team in understanding the work flow of the application.
• Developed the business logic using Java.
• Used spring and hibernate for backend development.
• Design & development of web-based programs using HTML, JavaScript and CSS.
• Implemented MYSQL/PostgreSQL queries and MYSQL/PostgreSQL stored procedures, and built-in functions to retrieve and update data from the databases.
• Followed Agile methodology for rapid application development
• Used Eclipse Kepler for Code Development and Apache Tomcat7 deployment of the Project.
• Used Groovy based Apache Gadle for building and project automation
• Followed Test driven developed (TDD) throughout the application.
• Performed regression test to check for unintended errors after enhancement.
• Transitioned from Apache Maven to Gradle for previous modules of the project.

Of course, it’s not sufficient to be called a genius simply based on his extensive skills in programming. Vyshakh is a genius because he’s also performed music in NGOs, blind schools, and taught music to poor children.

Surrounded by geniuses- part 7 : Adam

adam matrix copy The Mysterious Genius of the Su Lab remained quite the mystery even after I’d been with the lab for a month. Where did he come from? Where does he vanish to? What is he working on? Given the extremely varied backgrounds of the other Su lab members, it would make sense if he was a member of a secret organization dedicated to liberating humans from machines hellbent on enslaving humanity. Were this the case…did I really write this post?

Fortunately, the Mysterious Genius, Adam Mark, doesn’t appear from and disappear into a higher plane of reality. He’s just making the painful commute between the Su lab at TSRI and San Diego State University, where he just completed his first year as an M.S. Candidate in Biomedical Informatics.

Enthusiastic about both bench work and programming, Adam would love to combine his two disparate skill sets to transcend the translational genomics and big data realm. The Mysterious Genius has been working on developing an R client for as well as

Don’t be fooled by the surfer dude vibe…Adam is unmistakably intelligent
An avid surfer and genuine connoisseur of ocean waves, the Mysterious Genius has traveled throughout Asia and the south pacific, and plans to make a trip to the Meditarranean soon. Not so mysterious, after all? Think again! The Mysterious Genius seems to be a beach-loving, wave-surfing, fun-in-the-sun, kind of genius, but further investigations reveal a colder, darker side to him.
Forget the hockey coach scouting Adam for his team, Adam became a coach himself
Throughout his undergrad, he played for SDSU’s ice hockey team and then went on to coach the sport for two years after graduating. After graduating, with a B.S. in biochemistry, Mysterious Genius joined Dr. Saloman’s lab at TSRI and even contributed to a publication in the prestigious journal, Science. Upon returning to SDSU for graduate studies, Mysterious Genius was recruited by the genius-in-charge with insane mental organizational skills to conduct his thesis research in Biomedical Informatics.

Surrounded by geniuses- part 6 : Karthik

This motley crew muddles through motley clues

The genius-in-charge with insane mental organizational skills described his collection of geniuses as a motley crew–a group of people of mixed background, especially one with a common goal (awesome science).

Although the group does have some things in common (they are geniuses…all of them), for the most part, they are quite different. Take the Insanely talented undergrad genius for example. Most members of the Su lab have completed or are on track to complete a graduate degree. This might be Karthik Gangavarapu’s case in a month or so, but right now, he has yet to finish his undergraduate degree.

How’s that for genius? The Insanely talented undergrad genius worked with the Su lab previously through the Google-hosted Summer of Code in 2012 and 2013, developing an interactive network visualization for data linking genes to diseases in Gene Wiki+.

If you have any doubts as to the appropriateness of the genius label, visit his personal site and see some of the artistic work he’s done with javascript. If you still don’t see it, consider this: Karthik was also one of the co-founders for Tune Patrol.

As for his membership in this motley crew, Karthik carries some experiences worthy of sharing with the Dos Equis guy. Imagine the commercial:

Be patient, mew soon as I find a way around your security, we can be together
Be patient, my love…as soon as I find a way around your security, we can be together

He once connected 150 bands to audiences…with his keyboard.
“He has feline fans stalking and preying to get his attention.”
“He was once in the service of a monkey. A real-life. Friggin’. Monkey.”
“He is the insanely talented undergrad.”
Insanely talented undergrad genius
 Karthik: “I don’t always wear neko mimi, but when I do, they’re ones that have been developed to read and express my emotions.”
As a member of the Su Lab, the insanely talented, undergrad genius has been working on the next tool in the developmental pipeline following his work on The Cure.
Much to his dismay, Karthik now sends telepathic waves that attracts members of the feline species since donning the famed Neko Mimi (helm slot, +8 INT, +4 CH, -2 STR)