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What is Benchfly?

Launched in late July, BenchFly is a web-based resource and holistic, everyday guide for the entire career of a scientist. We’re engaging and educating life and physical scientists with video protocols, peer-to-peer sharing, product info and science-life tools. Our mission is to support and celebrate the researcher’s life in and out of the lab to perpetuate the viability of the craft and keep scientists in science.

You can check out a video of our mission here.

“Chemist, Neuroscientist and Founder. . .” please tell us about where it all started and how it progressed.

I think it started in the kitchen when I was a kid- inspired by baking soda and vinegar. Growing up, I always gravitated towards math and science because they just made more sense to me. However, when I got to college, I decided it was time to see what else was out there. So I spent the first couple of years far from the laboratory. Eventually, I realized I just wasn’t cut out to perform Shakespeare or debate the meaning of self. I’m a science guy.

In fact, I’m a third generation chemist. I guess I inherited the chemistry gene from my father and grandfather. I grew up in and around the lab and it was certainly a powerful influence in the way my career evolved.

Whether studying organic chemistry at Trinity University, chemical biology at UCSF or neuroscience at MIT, I’ve always found the interface of fields to be very exciting. I started in synthetic organic chemistry, moved to biochemistry and virology and ended up in neuroscience. Now, I guess I’m taking all of that and mixing it with the internet. Maybe I should toss in a little baking soda. . .

What was the best aspect of lab life?

I really enjoy performing experiments and learning new techniques. To me, the process of discovery is very exciting- and of course, so is the discovery itself.

As an undergraduate, I worked with an incredible postdoc, Dr. Chad Peterson, who had great hands- every reaction he setup seemed to work. Although I didn’t realize it at the time, I was the beneficiary of the many tips and tricks he’d learned and developed over the years. Those techniques gave me the skills and confidence to keep going in science. Unfortunately, whether a student learns that kind of knowledge is pretty random- it depends on the lab, the project and the mentor.

A close second would be the huge paycheck. (Just seeing if you’re still paying attention …)

What didn’t work so well?

The process of learning new experiments. Unfortunately, when I graduated from college, Chad did not go with me… I was on my own and found out quickly that not everyone cares enough to take the time to teach the ins and outs of an experiment. When learning a new technique, I always found it frustrating to have to find someone who knew the technique, contact them, coordinate schedules with them and then hope that you took good notes when they showed you how to do the technique. Once you got through all of that, it still wasn’t clear if you were learning a good technique or not. I always felt there had to be a better way for scientists to learn laboratory techniques that wasn’t dependent on their location or surroundings.

My experience with Chad is really what I’m trying to recreate with BenchFly. I want scientists to feel that they have a mentor and partner in the lab committed to their success that can serve as a wealth of information to help guide them whether they’re just starting out in science, already in the trenches of grad school or cresting the climb in a postdoc. But unlike Chad, BenchFly never needs to eat or sleep . . . so we’re always there to help.

What is the most important quality in your opinion for a scientist?

A few qualities come to mind, but if I had to pick only one, I think I’d go with honesty. The damage done by a single dishonest scientist can be incredible. Not only will people waste time and money trying to reproduce bad work, but horrible stories of scientific misconduct always seem to garner the attention of mainstream media. So it hurts both our progress and our image. Bad and Bad.

How easy was it for you to “transform” from a scientist into an entrepreneur?

Well, if we’re talking transformation, I’d say I’m still in the larval stage . . .

It’s definitely not been easy, but there are a lot of parallels between being a scientist and an entrepreneur. In science, we identify a problem that interests us and that we think, if answered, will be a significant contribution to science/health/society/etc . . . Then we go about systematically figuring out how to solve the problem. What experiments can we run, what reagents do we need, what collaborators might help.

As an entrepreneur, I’ve taken a very similar approach to identifying and addressing a problem. In fact, I think scientists make great entrepreneurs in part because of our critical thinking skills.

Most importantly, I’ve been incredibly fortunate to have a fantastic group of mentors and advisers that I turn to for advice and guidance (like a good P.I.—to follow the science analogy). As with any successful scientist, it’s important to have support as an entrepreneur.

What are the hard parts?

Not knowing what decisions are critical is one of the hardest parts. After nearly 15 years at the bench, there is an ease and confidence in performing experiments that comes from experience. You know exactly which steps can kill the experiment. Starting out as an entrepreneur, it can be very difficult to know which decisions may end up setting you back. Once again, I’m incredibly grateful for my advisors—and the magic 8-ball . . .

What was the driving force behind BenchFly? When did the idea come to mind?

The idea was really born out of the pain of my own research experience. Although I had a great time at the bench, there are certainly things that could be changed that would make research better. BenchFly is my attempt to provide some of these resources for scientists and to support scientists lives both in and out of the lab.

An important part of the mission is to reinvent the image of the scientist. The pocket protector is dead! Scientists are some of the funniest, most intelligent, inquisitive, and generous people I know. The idea that we’re some socially inept group of creepy psychos locked up in the basement of buildings is outdated and ridiculous. Our image has profound implications for the way the public, and future generations, view our profession.

What has changed in your daily routine after starting BenchFly compared to your daily lab routine?

There’s been a complete inversion of my daily routine. Basically, anytime I used to be on my feet doing experiments, I’m now in front of a computer. Anytime I used to be checking my email in lab, I’m now standing up to stretch my legs. It’s been a bit of a shock to the system. And by “system” I mean the number of chins I have.

We are seeing various sites now offering video content for scientists- what’s your take on that?

I think video is the natural progression for all aspects of life. Video cameras are everywhere- in phones, iPods and computers. It’s not hard to imagine a world in the not-to-distant future where every second of everyone’s life could be recorded and uploaded. Of course, most of it would be more painful to watch than a Yanni concert, but the technology is basically here.

In science, video is such a powerful medium because it mimics the way we naturally learn and work in the lab. In an educational setting it’s particularly powerful given that the techniques and instruction can be watched repeatedly, on demand. Since instructional videos bring the expertise to you, it means you no longer have to be in “the right lab” to learn the proper techniques. It democratizes science.

What differentiates you from video protocol sites?

BenchFly is also different from other video sites because in addition to sharing insider knowledge we’re not afraid to have a point of view: We’re trying to knock down some of the stereotypes that learning science has to be serious and boring. I like that BenchFly represents and showcases to the world that science can be fun, irreverent and exciting. There’s a video on the site showing a grad student trying to eliminate static from a scale. Non-traditional science to say the least… but very valuable information.

Another one of my favorite videos on the site shows a trick for turning a solvent squirt bottle into a silica gel dispenser. It’s outstanding. If you’re a chemist, you know you can feel the years falling off the end of your life every time you open the drum of silica gel and get buried in the carcinogenic cloud of silica dust. But in 30 seconds, you learn a clever solution to the problem that you wouldn’t have otherwise known unless you were in the lab with this person. That’s the power of BenchFly as a resource to scientists. We’re helping pass insider knowledge to outsiders who want the inside scoop.

BenchFly is also more than just a video protocol site. While video is a main method to supporting scientists on the site, we also have two daily blog streams that address different aspects of a researcher’s life. Flyceum is the blog channel that focuses on professional and industry-wide issues facing scientists today. Some of our popular posts address topics such as: 10 Ways to be a Successful Scientist, How to Behave around the Boss, and Why Did I Become a Scientist. It’s been really great to see dialogue budding between scientists from all over and at different stages in the career path share their insights on things that affect all of us.

Our other blog channel, BenchLife, is more of a survival guide for balancing life at the bench with . . . wait for it . . . having a life. We’ve posted everything from talking about the challenges vs, benefits of owning a pet in grad school and quickie meal recipes to fashion etiquette for scientists and best practices for organizing your life.

BenchFly is synced with Facebook, Twitter and IntenseDebtate so it’s easy for scientists to comment and vote in our frequent “According to Scientists…” polls. The polls serve as a temperature reading on the scientific community’s view on a wide range of serious and (hopefully) amusing topics. Did you know that according to scientists the most requested lab superpower is the ability to control the outcome of every experiment?

We want to promote that scientists have a point of view and can tie science into daily life in a way that can make you laugh in the middle of a tough day in lab.

What are your expectations for BenchFly? Where it is going to be in ten years?

One day, we’ll be able to think of anything scientific – be it a protocol, a paper or a legendary lab prank, search for it, and find a video about it. In ten years, I hope BenchFly is that site for scientists. I hope we’re actively engaging and supporting scientists worldwide. We’ve got some exciting announcements coming up very soon and some big dreams so let’s revisit this conversation in 2019 and let’s see how things turned out! In the meantime, please check us out at www.benchfly.com.

During the time I spent researching with Professor Zach Adam at Hebrew University, I visited Dr. Ralph Bock’s lab at the Max Planck Institute in Germany to learn how to transform plastids (see plastid transformation protocol). It was a relatively new method, and I was eager to learn all that I could. My main concern was that I would miss something and upon my return to Israel, I would be unable to recreate what I had learned. I remember the surprise of my German colleagues when I pulled out my camera, and began to take photos of every step of the procedure. Visiting the Institute was a great learning experience, and when I returned my fellow lab members had a step-by-step photographed protocol depicting how plastids can be transformed.

Today, with the rise of video protocol sites, my method of protocol documentation seems old-fashioned. Sites like BenchFly and JoVE (Journal of Visualized Experiments) offer the possibility to capture how science is being conducted and sharing it with the rest of the scientific community. Aside from sharing knowledge between scientists, Benchfly (free) also offers a glimpse of scientific procedure to those in the non-scientific community. I think its actually pretty cool.

• Watch How to mail DNA on BenchFly.
• Watch How to make a bacterial spreader on BenchFly.

I hope the research community will continue to see more content like this as it promotes and simplifies scientific research. In fact, we are seriously considering embedding video content to BioKM™ as external widgets.

Hats off to the people taking charge in creating and sharing their knowledge and taking the time to record and upload these videos.

Follow on Twitter:

• @BenchFly
• @JoVEJournal

Labor day has come and gone, and while summer doesn’t officially leave us until September 21st, we can agree, for all practical purposes, that the season has in fact come to an end. Just in time for the beginning of the academic year, I enlisted the help of my fellow researchers and scientists on twitter to share their advice with new students in the science field. The following is a short compilation of their words of wisdom.

Choose a good adviser:

Probably the most popular tip I received emphasized the necessity of working with a good adviser. @PolymerPhD suggests that students choose their adviser wisely. “Your adviser must ideally fulfill the roles of mentor, teacher, colleague, boss, friend, and advocate all at once. This is the person who will guide you in your research.” Brian Krueger (@LabSpaces) recommends listening carefully to what other students and faculty tell you about potential mentors as there are “lots of horrible slave drivers in science.”

Communicate with your adviser:

Once you find an adviser, many suggested that you do your utmost to keep him or her happy. As Dr. Zen Faulkes (@DoctorZen) pointed out, “Grad school is all about making personal connections” Even more important is staying in touch with your adviser and making sure to keep him involved in your work. While some advisers are incredibly busy, BioData’s Hamutal Lotan stresses the importance of making sure to set up (and pursue if needed) routine meetings with him to make sure you don’t lose track of your work and so that you know where it should be headed.

Be persistent:

As any person involved in research and science can tell you, its not easy and it will take a lot of time and patience to get results that work. At some point, Dr. Faulkes warns, writing your thesis or dissertation will feel like unending river of pain, but Dr. Josef Ashkenazi (@yossipossi) encourages new students not to give up easily when they have difficulties. @Toraks reminds you that your PhD “is a marathon, not a sprint. Work steadily & hard throughout—don’t burn out immediately!” Another way to cope with constant adjustments in the lab is to be flexible says Christie Wilcox (@NerdyChristie), “Things change a lot – whether it is funding or experiments. You have to be able to adapt.”

Learn from the experiences of others:

After hearing all sorts of ideas, I have concluded that the best advice I would give to new grad students is to consult with other students and learn from their experiences and mistakes. Who better to help you through the long process of grad school and PhD student than those who have been there before you? Just be wary of the advice you do receive, Jonathan Gross (@rubp) cautions – make sure you ask advice from the right people as bad advice can cost you valuable time and cause unnecessary frustration.

Other tips worth mentioning:

• Read, read, and read some more. (@Aquafloriana)

• Read a book that demonstrates the art of reading journals, organizing their thoughts and designing experiments. (@ScienceLifeNY)

• Read, think, and experiment broadly. Narrow specialization is for postdocs. (@Boraz)

• Use all your intelligence and passion to take ownership of your project! (@Epigenetique)

• Formulate an innovative and testable hypothesis ASAP! (@RibogeniX)

• To decrease future frustrations, eliminate unknowns in your power like contaminated buffers and wrong reagents. (@ScienceLifeNY)

• Make sure you know not only what you’re working on, but also the general field & how your work fits in. (@toraks)

Find more tips for new students on @BitesizeBio’s blog which provides pointers for new grad students as well as do’s and don’ts for PhD students. @Aemonten also wrote an article with a few ideas for grad students to keep in mind.

Results and Analysis of BioData’s Laboratory Management Survey

In a survey commissioned by BioData, 94 researchers from 74 institutions worldwide were asked a series of questions regarding their management of research data. The survey’s purpose was to learn about and prove the need for knowledge management systems in academic research. 80% of the researchers surveyed believe their labs are not run efficiently.

William Noble, associate professor in the Department of Genome Sciences at the University of Washington recently published “A Quick Guide to Organizing Computational Biology Projects,” an article dealing with management of data related to the bioinformatics field. When one thinks about managing laboratory data, it can be overwhelming to think of all the files, graphs, images, and results that come with every experiment. Noble explains that while organizing files and documenting progress seem mundane, “These issues are important because poor organizational choices can lead to significantly slower research progress.”

Over the past two years, BioData has worked with over 30 research groups providing them with a research management service. Dr. Noble may be referring to actual management of files and folder, but we have learned that having a systematic way of organizing results and data, promotes research and makes the lab a more pleasant work place.

Data Organization

Data organization is key to saving time and frustration when you don’t have to waste time looking for where you stored everything. As one frustrated PhD student expressed, “I have got so much data on a thousand different machines… and I cannot keep track of it all. I do not remember what I save to what or where it is, whether I’ve backed it up or not. Anytime I’m getting ready for a conference, presentation, or review I spend hours and hours just trying to find everything! Everything else in my life is overly organized except the one thing that is most important—my RESEARCH! I dread having to write my thesis because I don’t think I’ll be able to find all my data…” If your data is organized and stored in one place, it is easy to keep track of and access whenever you need it.

Another reason why data organization is so important, Noble explains, is that “someone unfamiliar with your project should be able to look at your computer files and understand in detail what you did and why.” As one researcher told us, “… Each lab is left to its own devices to archive data and institutional knowledge. As per usual, experiments get repeated as grad students graduate and new ones come in…” When a new researcher joins the lab, they can easily see what you worked on, so time and money is saved by not having repeat experiments conducted. Noble cites other people who may be interested in viewing your laboratory data: “This ‘someone’ could be any of a variety of people: someone who read your published article and wants to try to reproduce your work, a collaborator who wants to understand the details of your experiments, a future student working in your lab who wants to extend your work after you have moved on to a new job, your research advisor, who may be interested in understanding your work or who may be evaluating your research skills.” The most important person, Noble points out is your data needs to be organized, for yourself because after a couple of months, your likely to forget details and “you will either have to then spend time reconstructing your previous experiments or lose whatever insights you gained from those experiments.”

Keeping all of your data in context is hard. We see researchers running three to five experiments concurrently, spending hours on collecting results – but neglect to document it properly. Documenting data may seem like a tedious, wasteful step, but each researcher must think of its long-term benefits, as it is the one of the main qualities seen in organized labs

Data also has to be accessible and stored securely. 56% of the researchers surveyed stored their data on a hard drive. There is a problem with storing data in one place, as many learned the hard way from Hurricane Katrina, when an incredible amount of data was lost. One researcher from New Orleans’ Tulane University pointed out, “Before Hurricane Katrina, there was no backup system at all. Now, they issued everyone a 80GB external drive and gave them stern warnings that there would be no rescue missions for hard drives if another levee breach occurred… Surely we can do better than this.”

Online Data Storage

Noble suggests storing data online, as hard drives cannot be accessed once you are out of the lab, and as another researcher pointed out “I think there should be online storage of research data … so when ever you have time you can analyze your data.” In fact, 80% of researchers said they would store data online in a secure server, with many expressing concerns about security, citing a need for “a rock solid privacy policy and some serious security.”

We learned from this survey that many are in need of an online knowledge management tool that is safe and secure. While the importance of data organization may have been overlooked, researchers are now becoming more aware of its role in running an efficient and productive lab.

BioData is committed to helping researchers in the scientific community optimize and manage their knowledge and data. To learn more about BioData’s online knowledge management tool visit www.biodata.com

Read “A Quick Guide to Organizing Computational Biology Projects”

Noble, W. (2009). A Quick Guide to Organizing Computational Biology Projects PLoS Computational Biology, 5 (7) DOI: 10.1371/journal.pcbi.1000424