28 July 2011

Research and Impact

Whenever one starts a new activity or challenge in life it affects the person who undertook it.  This change can happen in small ways or large ways but it happens.  Then how does research fall into this catagory?  Most people, when they think about research and scientists consider an image of a man who is middle aged or older with some facial hair who's unkempt, wearing a white lab coat, and typically with scientific instruments or equipment, books, filing cabinets along with some phrase like eureka or formulae (here is a study that includes a section on the public image of scientists).  However there is so much more to scientists, where they work and who they are.  An example would be the lab in which the current project is being worked on.  Professor Han's lab is filled with diverse people who all enjoy their research but also enjoy other activities as well.  In terms of research, while it does involve a lot of work as well as books, equipment, and filing cabinets to keep everything organized and perform experiments, there is so much more to research.  It involves a creative mind to approach problems and it involves a lot of cooperation and collaboration, research is social.

Having entered a research lab, one learns more about scientists, research, and one's own competence in research.  After one has entered a lab, worked in it, and had the chance to assimilate, a wonderful event occurs.  Research can be done!  The trick with research is to endure, be open and willing to learn, and to try one's best.  If this is done then a niche can be made in the lab.  Research is definitely challenging but so are numerous other things.  It is a great experience to enter a lab and to then develop a sense of competence through such an experience.

The research experience can be brought to the classroom as well, a way to disseminate information.  Research is a mix of times of patience and hardwork and times of problem solving and creativity.  Having moments in the classroom with problem based learning is a way to convey some of the ideas involved with research in the classroom.  These introduce problems and then encourage creative and critical thinking just as research does in a lab.  Another way is to have moments that require looking up information and then critically considering the information, not just to write down every fact that appears but to analyze and filter it.  Just like in research, it is important to know which information is pertinant for a project.  Bringing in ideas and topics in modern day research is way to bring research to the classroom while connecting to the present day and making information more modern.

There is a lot involved with research and it is a fun and extraordinary journey to explore.

27 July 2011

Lab Meetings

In many labs, there are group meetings for the entire lab.  How often these happen depends on each individual lab as well as schedules.  For this research group, these meetings happen an average of once per week.  However these meetings can happen more frequently if there is a lot of work to be done on a project and less often if members of the lab are going to conferences, working more independently on their own separate projects, or are time crunched in activities that are time sensative.

What can happen in a group meeting?  These meetings can be used as a way to check in with some of the other projects happening in the lab, as there are typically several projects happening in one lab.  An example would be several members of the lab group giving short couple minute presentations on what they have been doing, some data, and other important points for their project.  This not only informs the rest of the group what is happening but also opens it up to the group to help talk out possible problems and offer an outside eye to the project.

Another way group meetings can be used is to share information.  If the lab is a neuroengineering lab, such as the one with the current project, then having weekly talks about the different parts of the brain and how they function.  These would be beneficial for the whole lab and are good general knowledge for all of the members to develop.  These meetings also give valuable experience for the presenting members since giving talks in science is an important media of communications in the scientific community.

Group meetings are also used to disseminate information.  These can be used to inform members if and when other events are happening as well as updates or changes in protocol.  Members from the lab can even demonstrate a technique which is important for the whole lab to understand.

These meetings also help to build a sense of community in the lab.  During the last group meeting professor Han made a great statement about the lab: that any problems are not just those of the individual member but are something that are a part of the whole lab, it should not just be someone else's problem.  She is very encouraging of the individual members as well as the members as a whole.  Research is both cooperation and collaboration between people and it is important to foster a community that allows both.

26 July 2011


When building something yourself and thus ordering materials it is always a good idea to keep a list of materials for yourself and what the materials are meant to be used for.  If you are ordering three different lengths of bar then knowing which length applies to which part of the object you are building makes one's work lighter later on.  Once all of the materials arrive it is then time to actually build whatever is to be built.

In research when getting orders for a research project they are not typically sent to the lab, they are actually sent to another location for pick up.  Once arrived, members from the lab pick up the materials, bring them over to the lab, and then check to see that everything has arrived.  Members look at their lists, compare them to the materials, and compare those to the receipts.  The receipts are then kept in a safe location.  Then build begins.

For the current research the object to be built is a box.  Before building it is good to consider how the object has to be built in order to stand on its own.  First the outside skeleton has to be built so that all of the siding and caging can be attached.  This way the walls can simply slide into place and the caging is firmly attached, the mouse after all will be walking over the caging so there should not be any sagging.  After the outer structure is finished the side walls have to be cut down to size; be snug enough for no movement but small enough to slide in and allow changing of the set up.  As with any project, it is important that all of the pieces fit perfectly.  After making the sides and having the box generally finished except for the sensors it was checked over.

In research and in building, especially if one is trying to create the most versatile object for a purpose or in setting up, collecting, and analyzing data, it is important to have open eyes.  This means that one is constantly evaluating the process.  For the box this means that if it has come together and then another point is requested such as sliding in the devices, then the box should be changed to suit this new challenge.  Likewise, during build if a better way to create the box presents itself the idea should be seriously considered and not simply brushed away because it is not the plan.  This can also be applied to taking data in an experiment.  When collecting data, if something looks wrong it is prudent to stop and think for a moment before proceeding.  Data that looks wrong can be due to numerous factors from a slight miscalculation of the data to adjusting how the data is collected to discovering that samples may have become contaminated.  Catching some of these errors during data collection can save time in the long run even if it causes a momentary pause.

After the initial box was completed, and after checking in with other members of the lab, it was decided to rearrange the box to allow for more interchangeable parts since this box is to be used not just for ports but with a monitor as well.  Therefore part of the box was taken apart, reassembled, and then put back together to the current set up.

With the box as it stands right now, the next step is to determine the best and easiest way to set the sensors up.  In many research labs a bigger project will be broken into smaller parts that need to be handled along the same timeline.  This is true for the box which is a smaller part of the larger project.  Currently, as the box prepared to move into phase two in inserting the sensors another member is working on the programming for the system. The programming language has changed to MATLAB now since this is the language that the programmer is most comfortable with for this project.  It is by dividing the work into manageable parts with people who have skills in the different areas, such as some members building a box and others with the programing that a project is able to be completed with a good timetable as well.

14 July 2011

What is the Research?

When doing a research project, it is important to know what you are testing, what controls are involved in that testing, how the results will actually be measured, and what is the reliability of the data.  This process not only applies to the research at large but typically to many of sub-projects for an experiment as well.

What is being tested in the box experiment, or the hypothesis, is whether it is possible to build a cheaper testing box then the ones commercially available for the mice that can be used effectively in the mouse training and observing experiments.  This idea is important because in research labs where funding is always something to be aware of a way to perform the experiment to its maximum and save money is always the preferred way.

As with any experiment there is a control, which is the box that is commercially available, which will be used for comparison.  This way the box is not left on its own in assessing performance with respect to the mice but has a standard to uphold.

The measure of success will come from the comparison between the two systems.  First will be the cost difference between the two systems.  Will it really be time effective and cost effective to build our own system versus purchasing the commercial one?   Next will be if the mice can actually train in this cage.  If the mice cannot train then the box did not succeed in its purpose.  There will also be a comparison of how data is collected and if it is working effectively.  Are all of the interactions of the mice being registered in the system?  By looking at all of these facets the results can be analyzed and it can be determined if the hypothesis was met.

Finally, how reliable is the information and data collected?  In any experiment if the data in unreliable then one has no way of trusting the data and therefore cannot make full conclusions.  In order to ensure how reliable the data for the project is the box will be checked at several stages for how well data is collected from the mice such as whether or not the mouse can even function in the prototype followed up afterwards when the box is finished by whether or not the box is functioning for the mouse as well and then afterwards checking the data on the mice and whether it matches what is being visually seen with the collected data.  In an experiment the end product is just as important and sometimes more important than how the experiment begins but this truly cannot be determined unless there are ways to determine successes and failures.  One can learn just as much from successes as failures if all is documented and properly followed.


Since the project for this experiment is having a final box for training and taking data about the mice then there are steps that are involved with building the piece of equipment for the lab.

The first step, building a prototype, was completed during the first week.  A good prototype is something that is relatively cheap and easy to make but allows the user to evaluate how effective the instrument will be.  For this project a prototype box was build using a mixture of metal bars, brackets, and screws that will be used in the final set up along with cardboard for the walls to gauge dimensions and practicality of the box.  The box will soon be tested with some actual mice to check the viability of the set up.

Having built the prototype of the box, the next step is to build the actual box itself.  To do this step however requires a small side step, the creating of a materials list.  This side step is where the first wave of patience plays is part.  When making a materials list it is important to know what materials are needed, how many of each item, as well as the vendors that are being purchased from.  This process can take some time to complete.  First is the fact that funding for research comes largely from grants which sometimes can have limitations on who and where items can be bought from.  After sorting out the limitations on the grant if they exist (which luckily for this project did not), then begins the search for the right materials and prices.  Since there is only so much money in grants, the bulk of the time compiling a materials list is looking for some thrifty finds that are from reliable locations that can also be sent within a reasonable time to build the box.  How long does it take to compile a materials list?  It certainly depends on what the project is but for this project took approximately a day and a half.  This included meeting with our principle investigator (PI) Xue Han and one of the post doctoral fellows (post docs) in her lab about materials, then searching for materials, followed by a discussion with the post doc and other members in the lab about options for some of the materials.  This was followed by more searching when one of the items changed slightly, another discussion with the post doc to double check the list and one final search and decision on materials since there was another item that was decided to add to the list.  Then the list was organized in a way easily understood to expedite the process and then sending out the order.

Now that the materials have been ordered, patience is what is needed until the materials arrive.  What is done until then?  Time is definitely a commodity in the research lab so it should be used wisely.  While waiting for materials to arrive the best course of action is to start working on the next step of the process, and if that is not possible, preparing for the next step in the process.

What has been done since the ordering?  The next step for this project is creating an understanding of Labview, a graphical computing tool, to help in programming the box once it has been put together and functioning.  It is the Labview program which recognizes when the mice initiate the trial and then runs the devices and collects the data about the mice and the box.

How does one even start to learn a programming language like Labview?  What we did was get copies of the current programs running for the mice trials, print out copies to write on, and then started dissecting the program.  One of the great things about programming is that once you have learned some computer programming, no matter the language, it starts to get easier and easier in learning new ones.  Many computer programming languages use similar constructs, even if they are worded or look a little different.  Before fully dissecting the program it helps to build first a general knowledge of the program itself.  Simply run a search for the basics and begin the process.  For Labview we found some basics on the National Instruments website along with a couple of others that explained some simple programs.  If your a visual learner, it helps to find videos with some examples (such as the National Instruments website had).  After that, with the basic knowledge in hand, to dissect the program involves both looking at the program with the icons and connections as well as searching for what certain objects are doing and what their functions are, then going back to the program and piecing together the meaning.  When attempting to create meaning out of a program it is vital to understand what the purpose of the program is and what the program is ultimately supposed to do.  If these items are not known, it will dramatically increase the difficulty of gaining a full understanding of the program.  After doing all one can, if possible, it is great to talk to the program creator or the one in charge of it to ask any questions that may have appeared and checking one's understanding of the program.  However learning programming is like an exponential curve and it, too, takes patience.

08 July 2011

Entering a New Lab

So as with entering a new lab it helps to know what the different research topics are in the lab and the general idea of the lab.  Then comes familiarizing oneself with the technical jargon for the research, meeting new team members, and catching up to speed with the work in the lab.  And of course, it helps to do a bit of research on one's own to help jump start understanding.

The lab I joined for the summer 2011 was Xue Han's lab.  She works in Biomedical Engineering (BME) as well as neuroscience.  The current idea that leads this lab involves treating brain disorders.  Such disorders are prevalent in society today, however in terms of medical treatment society is still lacking in the ability to treat these problems effectively.  Numerous disorders are untreatable and those that are have side effects on the patients.  Using optogenetics, the lab is searching for causal links between the neurons in the brain and physical behavior (like movement, decision making, attention, and memory).  To do this the lab is studying mice and their behaviors.  Ed Boyden has published several papers with Xue Han and in the video below discusses how optogenetics might help in this situation.

What we are doing specifically is to help create the training apparatus for the mice that is more complicated than what the mice are currently training with.  The main premise is that there is a port where the mouse pokes its nose in to activate a trial and then some lights will light up on the opposite side of the box where the mouse must activate the correct light for a reward.  Currently there is one activation port and one reward port and the goal is to add more ports than the one reward port so that the mouse has more choices to find the reward when activating the trial.  After training the mice then trials will be run and the mice studies for causality between the neurons in the brain and the behavior of the mouse.

The next step is to familiarize oneself more with the terminology and equipment in the lab.  This means for us that we had to review some Labview (a graphical computing program) which is currently being used to run the equipment.  It is through Labview that the lights work as well as the reward for the mouse's actions.  We also had to do a bit of research on this topic in science to create a better understanding of what we were doing (such as the video above).  This part of becoming accustomed to the lab definitely takes time and can be frustrating when other lab members already have this knowledge and one does not.  This part always takes time, a bit of patience, and a healthy curiosity for asking questions to create better understanding.

There are also challenges when entering a new lab.  Some of the more basic ones are learning people's names and discovering who to go to for questions; it is a team effort in labs.  One also needs to learn the layout of the lab, where the equipment is kept, where offices are, how to get materials, and how the experiments run.  It is definitely helpful to get a tour, such as we did, and to ask to observe some of the experiments and then ask questions as a trial runs.  Everyone in the lab is open and excited for the research as well as willing to answer questions.  Working as a team helps to keep these challenges down and encourages collaboration to solve problems that arise in the lab as well as creating new ideas to spring from in future experiments.

As for creating the apparatus, a good first step is to consider what the goals are for the device and then if there are any limitations.  For the device that we are building we are looking for a larger and slightly more complicated version of a set up that already exists so the basic layout is already known.  What we had to do was decide the dimensions for the set up which involves several measurements.  Therefore we first measured some of the parts already available in the lab and then chose the upper limit of width per side.  This limit is based off of a secondary set up that will also be used in the lab.  Then we needed to calculate how wide the panels for each port would be.  We took the entire decided width keeping in mind how much space is taken up by the panel joints and divided by the sides we wanted to have in the final set up.  Finally, before deciding if these measurements would work in terms of dimensions we created a model of the ports side of the apparatus.  To do this we cut out the dimensions on extra cardboard in the lab and then put them in order with the panel joints.  With the model we were then able to decide on the dimensions needed.