A valentine to the Applied Biosystems Veriti® Thermal Cycler

I can grow very attached to PCR machines. A large part of my undergraduate thesis revolved around running PCRs on Applied Biosystems machines and I was trained from a very young age to be very picky about where I put my reactions. After a few years of struggling with the lack of reliability and availability of the Bio-Rad Tetrads® we have in my post-doc lab, I just bought a couple of Applied Biosystems Veriti® Thermal Cyclers from Life Technologies. Granted it's just been a week and I'm still in that happy and dazed phase, but I can barely contain my excitement.

You know how as a child you see things adults have, and as a grown-up you buy the same things so that you feel like an adult? PCR machines are it for me: a lab is not a lab without one. We demoed a Veriti® last Fall and really liked it, then got an offer that we couldn't refuse with a bonus on the 2-for-1 end-of-year special, which made them really affordable.

What is so special? Well, first of all, as you can find in a handy video here, the Veriti® is really easy to use, you plug it in and 5 minutes later you are running your samples. The interface is completely intuitive and the touchscreen is very responsive. THEN, with the VeriFlex™ block you can use 6 separate temperatures for two 8-well strips at a time. This means not only that you can run a precise gradient to test your conditions, but also that you can run multiple reactions at different melting temperatures as long as the extension is the same. We tried both these things with our very difficult genotyping reaction and I almost wanted to cry it was so beautiful. We ran both the wild-type and knock-out reactions on the same block with a 50 and a 58 degree melting temp at each end and everything worked. Since some of our more complex breeding needs up to 4 different PCRs to capture all the alleles, we would be able to run everything at the same time on 1 or 2 machines. We have not tested neighboring strips yet for consistency and interference. They claim you can do completely different temperatures, but we just built a consecutive step gradient and used opposite ends so far.

Finally, apparently you can plug the machine into the Internet and there is software available so that you can run it remotely or have it send you an email when the reaction is done. This is a little creepy. I'm not sure I want a thermocycler to have that much control over my life, but it could be a handy feature if you are doing a lot of things and tend to forget, or if you're going out for dinner and want to know when to get back to the lab. Though I think the 4-10 degree hold should be sufficient for that...DNA is pretty stable....

Remember to look at the Lab-things we like page for more products and reviews.

Just because word clouds are cool....

Thanks to Wordle™at www.wordle.net

Submitting your R00 proposal to transfer your K99 to your new job: a survival guide

You were awarded a K99/R00 Transition to Independence award from the National Institutes of Health (NIH) and you even have a tenure-track job lined up!! You have survived writing your K99 and you think you got this whole NIH thing down. Think again...

The K99/R00 is an wonderful initiative that helps young investigators in training to complete their postdocs and transition to an independent position with almost as much money as a second start-up. You are NIH funded which increases your chances of getting a job in the first place, but the NIH never makes up codes in vain and the name K99/R00 means that you actually have to apply for the R00 portion.

If you have done your homework, you have talked to your Program Official at the NIH throughout your job negotiation process and have had them review and approve the terms of your job offer. In fact, they have helped you define what those terms should be so that they comply with the rules and regulations attached to your NIH funding, in the sense that no institution can shortchange you because you already have a K99. I have a lag of almost a year between signing an offer and starting my job, but 6 months before my move, my PO already had me thinking about the transition. The Program Announcement (PA-16-077 as of May 2016) states that "The application for the R00 phase of the award must be submitted no later than 2 months prior to the proposed activation date of the R00 award by the R00 phase grantee organization." However, as always you have to BUDGET TIME well in advance, because since you're not at your new institution yet, everything will take twice as long.

This is what you R00 application should include, with added suggestions from what I just went through:

• A new face page signed by the R00 phase institutional representative. This is pretty straightforward and Sponsored Programs at your new institution will do, but remember there may be hoops, multiple signatures may need to be collected, last minute questions that send you scrambling from answers, and NIH regulations require everyone on the grant to be trained on Financial Conflict of Interest and to sign disclaimers (which you may have done at your current institution, but need to redo for the new one, so say goodbye to an afternoon).
• A new project description page (the project summary or abstract should be updated to reflect current plans for the R00 phase). This is fine, just update.
• Detailed budget pages for a non-modular budget. This is uncharted territory for non-budget savvy and it took me almost 2 full days with the help of a very responsive administrator, despite the fact that I had templates to follow. The K99 budget is very easy, but the R00 includes salaries, equipment, supplies, animals and other odd and ends like publications and travel, and you need to think about it to justify every single dime. You need quotes for equipment, updated amounts for salaries and fringe, estimates for animal costs and supplies. It's one thing if you're there and you can sit next to someone and go through the numbers with them, but if you're not, it can take a while. Also see this post for salary percentage negotiations.
• Biographical sketches. Just update, but remember that if you already have personnel listed on the grant, they'll need biosketches too.
• Other support. Just update.
• A new Resources page. Ha! This was a piece of cake at your postdoc institution, where you just copied your boss' R01. At the new place you have to figure out what's in the cores, where exactly is the equipment you know is there and what kind of access you are going to have. Your facility needs may not be same as those of other people, so you either get multiple lists or you have to rely on multiple people to give you tidbits of information. And again, you are not there. I was lucky as everyone was extremely helpful, but I had friends who had to fly back to the new place and gather everything that they needed in person.
• A brief description of progress made during the K99 phase that will serve as the Final Progress Report for the K99 phase. If you did a Year 1 report, it's the same format as described in the Program Announcement, but just a final report. You better have done some of the work, because I heard the NIH can give you grief if you have not actually worked on the project.
• A final evaluation statement by the K99 phase mentor. Nice long letter detailing how wonderful you are and all the mentoring you received during the mentoring phase. Basically take the mentoring plan and rewrite it in the past tense.
• An updated research plan (the specific aims should be updated to reflect current plans for the R00 phase and the updated research plan should be briefly described in less than 5 pages). I heard conflicting reports on this: some people submitted a slightly modified version of the K99 proposal continuing on that work and some had to do a major overhaul which is equivalent to writing a new grant. I did a pretty substantial rewrite adding new experiments to follow up the old Specific Aims, so it was time consuming. In general I find short formats much more difficult to write and 5 pages for Significance, Innovation, and Approach including Preliminary Data is not much.
• A letter from the R00 Department or Division Chairman describing the R00 institution's commitment to the candidate and plans for his/her career development. This is similar to the institutional commitment letter for the K99 portion, but it should relate to your new institution. It should also detail the search process to get to you as the best candidate for the position, describe your hiring package and the faculty development programs at the new place. Chairs are busy...letters take time.
• A new checklist. Sponsored Programs will do when they assemble the application.
• IACUC or IRB approval. If you work with vertebrates or humans they will ask you for your protocol approval. If you are like most people you will not have started these in advance, but beware since they may hold up your grant until these are approved, which could mean another couple of months.

A friend told me it took much longer that she had anticipated and she was absolutely right. You are getting ready to leave and you have a million and a half things to do in the lab, in addition to dealing with moving your personal life somewhere else. It is true that the R00 is reviewed internally and it's not going to a study section, BUT it's still a major NIH grant and you are asking the government for $750,000, so it should be done well.  Also remember a little known secret, the unspent part of your K99 will go away if you transition earlier than the 2 years, so be warned.

I'll follow up on what happens with my application. Remember to visit the Writing Grants page for more posts and links.
Note: around 5 weeks after submission my R00 was approved with flying colors....and no funding was cut because of sequestration! 

Some things I've learned from communication breakdowns

In the past few months we have had a few major communication breakdowns that severely affected a part of the project. Experiments were working erratically and when we started troubleshooting, we discovered multiple issues. Standard operating procedures were not set up correctly or changed because of outside advice and experiments were conducted in a sub-optimal (or not greatly controlled) way. Reagents were not working as they used to, but nobody noticed or thought that it was important to mention it and get it rectified. All this cost money, long hours of work to do the experiments in the first place and more hours to perform controls to figure out what was happening, call companies to discuss reagent issues, and it eventually delayed the completion of our project.

The breakdown of communication happened at multiple levels:

1) Incomplete Pass: I, in the first place, ignored one of the most common advice given to a new investigator: "Your hires are not you". I assumed wrongly that something was obvious, because it was obvious TO ME, when in reality it was not obvious for the person asked to perform the task. I did not double check the protocol or personally follow the experiment the first time. I trusted the trainee with a new task and the task was performed wrongly for a couple of months until someone else came in and saw what was going on. Once that I realized what happened, I could only be angry at myself, because I had made an assumption that they were going to read my mind.

2) Sideways Interference: Someone else recommended a protocol which was used for while and I thought my protocol was being used. The new protocol missed a few key steps which could have led to the observed variability in the results. I had trusted that my protocol was being used and was completely blindsided.

3) Unforeseen Sack: We received a few new reagents in October and I heard that they were not performing perfectly, but it wasn't until I had to run that type of experiment myself in early January, that I realized that there was something terribly wrong. Emails, phone calls, hours of tests and 3 weeks later we figured out what the problem was.
The vendor: Yeah, we've been having issues with it depending on the lot.
The New PI: But I've been using this reagent for 10 years and never had an issue. We compared it with the new, improved and recommended version a few months ago and they were identical.
The vendor: The new version is actually the old formulation because we changed formulations recently and the new one has this problem, but it still has the old name.
The New PI: Ah, I see. Can I return the bad stuff (new formulation/old name) and get some of the good stuff (old formulation/new name)?
The vendor: Sure! Here is a full refund!!
Despite the aggravation, the big problem here is that people noticed something was off, but nothing was done for months, actually making some experiments impossible because the reagent was so off to be unusable for some of our needs.

To continue with the football metaphor: What was wrong with the design of my plays? What is wrong with the team?
Two issues that I can see:
1) My players are rookies. They are learning and show a lot of promise, but they are at that training wheel phase when you can ride a bicycle pretty well and sometimes still lose control when the terrain gets rough. I failed to support them and follow them.
2) My plays need better planning and more coaching. During leadership training, I learned that good leaders have contingency plans and my plans have not been fully worked out yet. Also, I cannot just dole out instructions without making sure that people understand exactly how and why they are doing something. I still need to teach.

I guess I'll never stop learning how to manage people, but these were a few good months of errors to learn from.

Image credit: U.S. Navy photo by Mass Communication Specialist 2nd Class Herbert D. Banks Jr. [Public domain], via Wikimedia Commons

Millipore SNAP i.d. protein detection system

SNAP i.d. is a vacuum-driven apparatus to block, stain and wash your Western blots. It promises to shorten your time to as little as 30 minutes from the moment you finish your transfer to the moment you are ready for detection. It's definitely a significant improvement from almost 24 hours.

The concept is simple you put your membrane in a special cassette which allows even distribution of liquids, you first put the block on top and the vacuum sucks it through, then you continue with the primary antibody, etc. Blocking takes the time for 30ml of solution to flow through the system and antibody stainings which are done in 3 mL of liquid are 15 minutes. Washes are immediate. There is even a little plastic collector you can put under the cassette to recover your antibody, if you wish.

Does it work? Yes. We were really on the fence on whether we wanted to buy it. At $1,500 it is not cheap, but would it provide such huge time savings to be worth the price? If you are a biochemistry lab working on a finite set of antibodies and repeating the same assays over and over again, absolutely. We calculated the cost per run and since the antibody itself is the most expensive fraction of the cost, the $2 per cassette is quickly compensated by having to use less total antibody (though they recommend 3X concentration). At the end the cost per run is the same with traditional methods than with the SNAP i.d. In addition, cassettes can be reused a few times for the same antibody which would make it even cheaper.

Scilogex Analog Tube Roller

The problem is optimization. Every antibody must be optimized as far as concentration and incubation time. Reviews on the internet (here and here) indicate that sometimes you cannot skip the usual overnight primary incubation because the fast antibody absorption just doesn't work and that you have to play with the antibody concentration because of reduced sensitivity. One possibility we considered is to use it just for secondaries, which would shorten the washes-secondary-washes portion to 20 minutes instead of 3 hours.

As a new lab, I decided to pass for the moment because the upfront cost and the cost of consumables does not justify the expense. Instead we bought a Scilogex tube roller, which cost around $250, so that we could incubate our primaries in rolling Falcon tubes instead of shaking plastic cassettes cutting down the antibody solution to 2-3mL at the usual concentration, which saves us from using the 3X concentration required from the SNAP i.d. And the thing about the tube roller is that you can use it for a lot of other things. One day when I am rich, I'll buy a SNAP i.d.

Remember to look at the Lab-things we like page for more products and reviews.

Establishing lab culture in a new lab

Every time a common supply is finished and not reordered, or a common piece of equipment is broken, a little voice goes off in my head "When I have my own lab, this will not happen!". But, will it? And if it does, what do I do about it?

It comes down more generally to the lab culture, that set of rules which will reflect how you like to do science, how the lab will be run, how the lab members will interact with each other and conduct their experiments. A survey published a few months ago in the Harvard Business Review (here) showed how employees would follow a particular culture or strategy only when it originated directly from top management and how middle managers were often powerless to implement change by themselves. I have seen similar situations in multiple occasions, where things will run amok unless the Principal Investigator provides a set of credible boundaries. Lab culture is very important and as a new PI you get to establish and refine your own. It seems that in general lab culture reflects how the PI likes to work whether it's a conscious or unconscious effort, but recognizing the way you like things to be done, making an effort to establish positive culture and/or just to hiring people who will fit nicely in the existing culture can make all the difference.

A good culture promotes cohesiveness and assures you that experiments are done the way you want and with appropriate controls. So, I started thinking about what I would want for my own lab:

COMMON PROTOCOLS AND REAGENTS: I have worked in labs where you could not deviate from protocols currently used and labs where everyone had their own protocols, reagents, sometimes equipment and you could even choose whether you'd prefer to run your DNA gels with TBE or TAE. As a small lab having common reagents is a must and I believe maintaining common stocks promotes responsibility towards your fellow lab members. I also think there should be a reference folder with common protocols, which everyone can access. At the same time, protocols are often in flux as improvements and new reagents are used, so innovation must be taken into account and people have to be free to change and provide updated versions of common protocols. The risk of an extremely individualized environment is the complete loss of knowledge (and custom reagents) once an lab member leaves.

Image appropriately taken from a BLOTTR article on copyright

SHARING DATA AND IDEAS: There are lines of research where you can be 2 years ahead of everyone else and others where you could have toiled for 5 years to get to a major finding that someone else can reproduce in 2 weeks, so when and what to share is sometimes a tough decision. Personally I prefer being in an environment open to sharing information, because I believe results will come faster if you can work with others, discuss ideas and involve collaborators. I have been in situations where I had to think long and hard before sharing a piece of data and where multiple emails of mutual assurances of honesty had to cross before data was shared with me. I look at it like running a small business: if you work retail, you factor a percentage of your profits lost to theft, and if you provide a service, there will be cases where you won't get paid and you won't be able to recover the loss. It is fundamentally the same in science: some people will steal your ideas and run with them, it's a fact. I just do not believe that this should stop you from sharing, since talking about your work, being part of a community, collaborating and discussing your results are some of the best parts of being a scientists, at least for me. For this reason I will be completely open to sharing and will push my people to do the same within the lab and outside.

WORKING TOGETHER: I am very gregarious, yet in the lab I am a loner. I have always worked alone on my own ideas, which sometimes made much slower and less productive than I would have wanted because there was simply too much work to do for a single person. Now that I have people working for me, everything goes so much faster and constant interactions allow us to keep asking the right questions instead of just plodding along. On the other hand, working in teams in the lab can lead to a lot of conflict if the team structure is not correct: two lead postdocs on the same project can be a recipe for disaster because of authorship attribution. So I am going to promote a combination of independence and teamwork. It will be good for lab members to help each other and be in each other's papers, but each student and postdoc should have a primary project which is only theirs in addition to a secondary project which is shared.

Now, I just need to figure out how to inventory and share all my protocols and reagents, and how to hire the right people....I see more posts in the future.

20% protected time to generate new ideas

A laboratory is a factory of innovation which should generate new ideas to move your field forward. As a new Principal Investigator (PI), I have to decide how to drive the advancement of my lab. While I have more projects in my head than hands to complete them, how do I teach the members of my lab independence and spur even more innovation?  In a new lab you do not have a lot of grant money or startup to just give away for random pilot projects, but I have always been in labs where I was given complete freedom to work on whatever I wanted, so I never had to deal with a PI imposing a project on me and I shudder at the idea. What if one of your lab peeps comes up with a really cool idea you would have never thought of yourself?

A few months ago I found out about the 20% rule in technology companies, where employees are given 20% of their time (one day a week) to work on whatever they please to keep them engaged and foster innovation. The idea is to give employees the freedom to think independently and without direction, and it is widely applied at Google, leading to the development of tools such as Gmail or software fixes they would not have had time to work on during regular hours (here). Dan Pink discusses this approach at length in his book Drive, where he explores new approaches to increase motivation which I discussed in a previous post. However, Pink was not the first person to mention such a strategy. In speaking with senior PIs at Harvard Medical School during a mentoring session, I found that giving a portion of protected time to their postdocs to develop their own projects is a common strategy: "From 9am to 5pm you work for me, after 5pm you work on whatever you want".  This allows the postdoc to explore new ideas for their own labs which are clearly distinct from the PI's, but at the same time furthers the PI's line of research and supplies data and publications.

Everyone always tells me "Your hires are not you!". Depending on their previous training, not everyone will want to take up the challenge to develop something new and a lot of money may be wasted in trying if the learning curve is not steep enough, which is a serious concern. At the same time it would be great exercise for grad students, and a step towards independence for post-docs. Large labs with vast resources can afford for some people to falter or take 5 years to to develop a new idea, because if 4 out of 15 postdocs generate data for 4 major publications a year, you are still doing exceptionally well. Also, large labs already normally attract very ambitious and independent young scientists looking for the freedom to develop their own ideas. As I have learned from friends and colleagues ahead of me, the new PI must be very careful about how their hires perform and how the money is spent. There are two primary requirements which should be met in a small lab trying the 20% rule: 1) the person given the freedom must be innately independent or have a history of independent thinking; and 2) the PI must be willing to take the time to learn about the new project and provide appropriate guidance.

One more thing to try which may lead to success or doom....

Remember to check out the Management page for more related posts.
Image: Wikimedia Commons

Words of wisdom for 2013: lab management tips

Boston fireworks

I thought I'd start the New Year with a collection of advice I have collected over the past few months. Every time I talk to a senior PI at work or at a conference or even at random dinner parties I ask for some words of wisdom, so here it goes.

1) HIRE SLOWLY. This seems to be the first and most common advice. Don't feel lonely in your empty lab and go hire the first person you can find. The first few hires determine the efficiency and the culture of the lab and the wrong people can sink a lot of money and ruin the energy.

2) HIRE PASSIONATE PEOPLE is a corollary to the first rule. In addition to having a good work ethics, the new hires must be passionate about science or if they are not already scientists, at least be passionate about something so that you can drive their passion for science. Non motivated employees are less productive, while passionate employees will be able to also drive others.

3) YOUR HIRES ARE NOT YOU. This is another very common advice. You cannot expect the same drive, passion and knowledge from everyone you hire. They don't know what you know and they are not supposed to. They may not think like you and have different learning processes. You have to learn to undestand other people's strengths and weakenesses and harness different ways of thinking to spur innovation.

4) COLLABORATE A LOT AND COLLABORATE WISELY. You are small and cannot do as much as you could in the big lab where you might have done your postdoc. Create a network of chosen people you can work with. Good collaborations may be hard to come by, but can be very productive and mean the difference in the level of publication. Budget a lot of time at the beginning to start and manage collaborations.

5) DON'T SAY "NO" FOR THE FIRST 2 YEARS, THEN START SAYING "NO". At first you have to accept every invitation to speak, to write something or to participate in your field because you need to establish yourself and get people to know you. Then after a couple of years you can start saying "No".

6) ENJOY THE START-UP WHILE IT LASTS. or 7) SAVE SOME OF YOUR START-UP FOR A RAINY DAY. #6 and 7 are in stark opposition and I'm not sure which one to pick. I've talked to people who have spent like crazy in the first few years to generate a lot of high profile data and others who have saved part of their start-up funds for 20 years to tie them over in a funding drought. Both approaches make sense and I guess it's like investing and you need to figure out how risk-averse you are.

These are the highlights for now and I will post more once I have new ones (here).

New Year's Resolutions: develop autonomy and promote innovation

While I like being in control as much as the next person, I tend to function well working with people who are self motivated and autonomous and I have little patience for people who are not. So in thinking about models for running the lab, I was immediately drawn to the concept of ROWE (Results Only Work Environment). A ROWE is a company focused on results, not on workplace structure: you work when you want, you leave when you want, you organize your day as you want, all that matters is that you generate the results you need. The emphasis being on flexibility and results, with the idea of fostering "freedom and responsibility" (see this article about Netflix unlimited vacation policy). This is not that much of a stretch, since most labs are run this way anyways. I have always worked in a ROWE, it fits my personality and so far I found that I do like people to tell me when they're coming in or taking days off, but once they keep me in the loop, I'm fine with anything they want to do as long as they're productive.

Climbing on the Potomac

However, this does not work for everyone and I have seen several people flounder when given no structure. In addition as an academic I will have to learn how to motivate students and teach them how science can be rewarding even when it's hard. While taking this pictures, I remember thinking these people were crazy carrying their kayaks on their heads up the rocks to run the rapids again, but isn't this the perfect metaphor for science? Spending most of your time carrying a heavy load up a rock-wall to experience the short thrill of discovery. How do you teach people that the thrill is worth the wait? And how do you keep them focused when they are given freedom?

My New Year's resolutions for the lab are to develop autonomy and promote innovation, but this is no small feat. Postdocs may be more likely fully autonomous and motivated, but technicians and students which will abund in a small new lab will still be figuring themselves out. So here are some more specific resolutions:

1) for the ROWE to work, we'll need to have specific goals set for everyone with a precise timeline. I don't necessarily have to set the goals for them if they are self-directed, but I'm a good enforcer and scheduler, so I can help them keep track

2) I should help them develop their organizational skills, so that they can schedule their experiments efficiently and plan their days productively

3) I need to learn to give people freedom to think, sit back and set them back on track when needed. This may be the hardest because I tend to want to jump in and help/direct, but it would be a good learning experience to have them figure things out through trial and error and develop their own ideas.

4) I need to listen: listen to ideas, listen to feedback, listen to grievances.

I will follow up in the Captain's log about how it goes.

myIDP: a SMART career development plan

Science Careers recently launched the myIDP website (here), which helps you define your Individual Development Plan, a blueprint for the next steps of your career in science. Though bare bones the site is brilliantly designed so that anyone can use it at any level of their scientific career from undergraduate to professor. The site starts with a questionnaire about yourself, your professional skills (communication, teamwork, level of focus, etc) and your values, and ranks different career options based on your answers. Interestingly I was almost evenly split between a academic staff scientist and a Principal Investigator, which is good because I am a staff scientist at the moment and I'll be a PI shortly...

If you are interested in exploring different careers you can go through the Career Exploration section or go directly to develop your Plan. You can set long term goal about career advancement or more specific goals about developing skills or finishing projects. The most important thing is that they have to be SMART goals: Specific, Measurable, Attainable/Actionable, Relevant, Time-bound. While "Get tenure" is certainly a career advancement goal and may be attainable, you need to break things down in little steps: "Apply for R01", "Teach X course to graduate students", "Publish paper #1", "Publish paper #2", and so on and so forth. Each of these larger goals can be broken into smaller goals with closer deadlines and with clear end-results. For each goal you have to define an accountability plan, which makes you really think about how to break things down. One of my goals has always been to "Read more papers" especially outside of my field, but sometimes there is just so much to do in the lab that skimming the weekly table of contents of major journals seems enough. So to make it doable I wrote "Read at least 4 new articles a week", which I know is not much, but some weeks feels like an achievement. I have a weekly reminder in my Asana schedule which needs to be checked off to make me accountable. And then there's finishing papers, lab renovations, grant deadlines and the likes which will come to you in a handy summary email every month.

After the planning, there is the implementing and for the Implement Plan you have to define your mentoring team. You not only define who your mentors are, but also what specific mentors are for: there may be people you talk to for job search advice, people you need to write letters for you, people who must teach you techniques. It is surprising how many mentors you can find and this exercise helps you identify areas where you may not have a specific mentor and where you may want to find one.

I like checking things off lists and when you ask yourself where you want to be in 5-10 years it's nice to be able to plan it out on paper. Early in my postdoc, I went to a grant writing seminar and they told us how you have to plan out your fellowship from the first year: early fellowship grants in year 1-2, career development awards in year 3-5, papers, job search. It stuck with me and I found it very useful advice, as sometimes I have seen colleagues miss opportunities because they did not think about the deadlines or time-limits involved.

In closing, thumbs up for myIDP. I'll do my best to have my techs, students and postdocs use it.

Remember to go to the Management page for more Career Development tips.
Photo credit: Sten Pose, Wikimedia Commons

Why we love Life Technologies Bolt gels

Lately we've been running A LOT of Western blots and our trusted Life Techologies rep, who always suggests new things to try, has been pushing the new Bolt Mini Gel Tank and the Bolt gels, so we bought one of the welcome packs (gel tank, 10 gels, running buffer, sample buffer, reducing agent and standards for $390). And a week later my tech begged for another one!

I only use Life Technologies Novex gels because despite the expense of the proprietary running buffer, they are better than the Bio-Rad ones and they were the only ones which worked well for mass spec band purification. The Novex NuPAGE gels cost the same as the Bio-Rad ones, but last longer and run very straight and crisp bands.

The Bolt tank and gels are completely redesigned. It's a double-length and narrow tank where gels are run side by side, which was strange at first, but this way you can only run a gel at a time with half the buffer. The tank also has a white background behind the gel to help you better see the loading. The Bolt gels have wells cut as wedges to make loading easier and to hold more sample than the Novex gels, AND Life Technologies lowered the price from $13 to $10 for Bolt. They run way faster, so that you can be done with a 4-12% gradient run in less than an hour. And last but not least, the bands are incredibly crisp (see the pictures comparing our samples run on the Novex vs Bolt). It kind of looks like a Christmas tree...

Note on 2/6/2013: After 3 months we found only one glitch. Running the gels at 160V as recommended makes the buffer too hot and causes some random gels to start melting deforming the front. We are lowering back to 120V as for the Novex.

Remember to look at the Lab things we like page for other reviews and cool products
  

End-of-year meetings?

Umberto Boccioni - Visioni Simultanee
(Simultaneous Points-of-view)

As we get closer to the end of the year, I have been thinking about having end-of-year individual meetings to discuss performance, expectations and general issues. During the first few years of my post-doc, my boss conducted yearly meetings to formally discuss the issues that you often do not discuss in science: Are you happy with the lab and with where you are in your career? What are your overall plans for your project and your career development? Do you need a raise? Which conferences do you want to attend?

It was a venue to air professional issues which only come up in passing, and it also forced you to make a summary of the past year and communicate your needs. It made it clear that it was okay to talk about what you want creating an open communication environment. I really liked it, because like a lot of people, I tend to be afraid of asking for things (help, money, advice, etc) and having a forum where I was expected and encouraged to identify what I needed was very empowering.

In addition, being always pressed for time, I realize I now tend to assign tasks without discussing their larger purpose within the project, so I have been trying to communicate more frequently on how everyone's work fits into the global scheme and I have seen how it immediately makes people more interested and engaged. I think it could be a good idea to establish biyearly meetings for my lab members: one comprehensive end-of-year and a 6-month review just to keep things going. It can be an occasion to discuss my vision for the lab so that everyone is aware of where we are going long-term, to address concerns people may have, to get to know their plans for the future, and to give feedback on behaviors needing improvement (giving feedback tips can be found here and here). To avoid giving a daunting corporate feel to the meeting I am holding the meetings over lunch and told them to pick whatever type of restaurant they like.

In preparation of the first of these meetings, I have been asking friends in business on how they like their performance to be assessed and discussed, and one friend raised the issue of "performance standard criteria". Companies have specific criteria for a specific job which must be met and the employee functions according to a framework where behavior and performance goals are set from the manager. This whole concept makes me break out into hives, because as a scientist I don't necessarily have a rigid structure to control my work and do not want one. However, I understand how it can be very reassuring to have performance standards and to know that you are doing a good job. We constantly function from deadline to deadline and have a self-imposed set of short and long-term goals which must be met. How do I develop that? And most importantly how do I teach others to streamline their work and set their own goals? What are appropriate performance standard criteria for scientists?....more posts will follow.

The Aztec Calendar Conundrum: organization and project management

As time becomes more and more limited and things to do multiply, I am looking for good ways to organize my days and projects and keep everything straight. I am starting to understand why PI's tend to ask the dreaded question "What am I looking at?". The student thinks their project is all important, but the PI has too much on her/his minds to remember exactly which experiment you are doing and want help on.

What to do when your calendar looks more like an Aztec one?
During the past year, I have tested a few different time and project management sites and here is what I found. This is in no way a comprehensive analysis, but just the results of hours of googling and trying.

HiTask.com

I used HiTask for 6 months and liked it a lot. It's a calendar, task manager and project manager all in one. You have a calendar where you can schedule events (talks, meetings, etc) and plan experiments. You have task manager where you can list everything you need to do and assign specific tasks to projects. And finally you have a project manager where you can invite your lab members and assign tasks to them directly. The calendar is nice and handy and the task manager is very straightforward (though not very organized once tasks are completed). You can assign priority levels, star specific tasks and keep track of a lot of different things.

Example from the HiTask website

Unfortunately, HiTask forbids me to use the site now because I have reached the maximum number of free tasks. There was no prior information on whether there was a limit to the free account and even if I went back and cancelled my tasks from 6-months before, it still didn't allow me to use it. This really annoyed me! To keep using the site I have to pay $8/month. If it was just me, I would have considered it because it's a very well designed site, but I think it's not worth it for the whole lab: $8/month for 5-10 people would be $480-960 a year and you'd have to remember to cancel whenever someone leaves or for temporary students. However, I would definitely recommend it for personal organization.

Asana

After HiTask, I went back online and I found Asana. After co-founder Dustin Moskowitz left Facebook, he created Asana, a project management platform to provide "a single version of the truth about what everyone is doing" (see more on Bloomberg BusinessWeek here).  Like the yoga pose it is named after, Asana may not be straightforward right away: it needs concentration and thinking on how and why you want to use it....it needs practice. But man, it is powerful and beautiful and completely customizable, and you can plan your entire life on it! And everyone else's life for that matter. And it is free for groups with less than 30 members.

The intro videos are very useful and in fact necessary, because you'd have no idea what to do without them. The help team is also very responsive. There are many ways to run Asana and organize your workspace: public and private. I split my workspace in Lab space and a personal space which is not accessible to others. In the Lab space I have pages for individual projects where each project is mapped out: I set headings for different parts of the project (Intracellular signaling, Learning and memory) and then use each task for a question that requires one large experiment each, e.g. Does my protein of interest regulate AKT signaling? Within each task you can set subtasks with specific due dates (Transfect cells, Drug treatment, Run Western) and keep adding them as many times as you need to repeat the experiment until the question is answered. You can then assign whole tasks or just subtasks to specific people, and lab members can plan their own work or expand on the assignment as they wish or assign tasks to you.
In addition of the individual project pages where you can generate an overview of what needs to be done, you then have your own task page where every task can be listed day by day independently of project so that you actually know how much you have to do. The organization of this page still needs some work, I think, since the sorting can be awkward and there is no calendar view to remind you of scheduled meetings and seminars. However, sorting my tasks for the day on Asana has become a routine by now. The only drawback is that it is not super user friendly and you would actually have to take the time to train people to use it.

Fun with data

Some more fun in the lab after all the management posts.
The other day after filling my undergrad's USB drive with confocal images, I decided we needed some more portable data storage. So I ended up buying animal shaped thumb drives for everyone....at $15 for a 8GB and $9-12 for 4GB at Staples sometimes data collection can be fun. They have a little chain to attach them to your ID strap or your keyring. I got the mouse, but could not find a zebrafish!!

Objection! Leading...And why Socrates would not like it.

Socrates teaching (detail: Raffaello Sanzio, Stanza della
Segnatura, Vatican Palace, Rome)

A few nights ago at dinner, a friend brought up an issue which stuck with me. She is a teacher and briefly mentioned how they try to avoid "leading questions" at faculty meetings, which made some of the other dinner guests comment on the high number of leading questions being asked at lab meeting. A leading question is designed to make someone say what you want or to influence their thinking, and it could be negative and sarcastic, such as "Don't you think you need some controls for that experiment before you can come to any conclusions?" Leading questions can be good or bad and they are closely monitored in the legal system and in journalism where the truth can be easily altered by how a certain person is questioned. Children and people who absolutely want to please are very vulnerable to leading questions as they will say what you want them to say, and may believe it too.

So I started thinking and realized that I ask a lot of leading questions! A leading question from a superior, maybe asked a bit too harshly because you're in a hurry, could stifle the impulse to bring new ideas to you. It may also not be the best way to promote critical thinking in students.

Researching questioning and teaching around the web, I bumped into an old friend, the Socratic method. The Greek philosopher Socrates had always been one of my favorites in high school, but he would not have approved of top-down way of teaching used back then in Italy. As detailed in the Dialogues of his pupil Plato, Socrates developed theories by constant discussion with his followers, often asking either broader or narrower questions to foster critical thinking and strive to fully understand a problem.

I found a great article about Socratic questioning in teaching and learning (here) with tips on how to pose Socratic questions and prepare for the discussion with students. Looking forward to trying.