Endgame

Typically research happens over periods of time with different grants and programs.  At the ends of these periods finished projects are expected, questions answered, and some results, conclusions, and discussions are conveyed.  In this regard of time period with end deliverables, a research project ends.  However, the idea and concept of the experiment does not disappear and in this sense, a research project will never end.  There will always be questions, the improvement of methods, and more information to be sought.  It is with these deliverables from research that society is able to create building blocks for future endeavers.

Therefore, when considering the end of a project one of the first considerations is the data.  Is it meaningful or not and why?  If a project collected data from contaminated samples then this situation cannot truly tell one reliable information on a phenomenon.  Part of determining whether or not data is meaningful also depends on how the meaningful is determined.  In problem solving, when a goal or solution is sought, conditions for reliable and successful solutions are also defined.  Consider the behavior box experiment.  The goal of the experiment was to create a box that allowed flexibility in the traditional way of training mice to later be studied using optogenetics that was automated.  Therefore, success is based on whether the box can function in the old sense of training with the mice and also if it allows some flexibility for the mice as well as the fact that its parts must all be automated to collect data.  As the project is drawing to a close the box is just about complete.  However, since the box is still being completed then it has yet to be fully tested with the mice and therefore there is no data yet for the box.  The data will be seen at a later time period after training the mice and observing the results of the training.  It is important to note that once the data is collected, that it is considered meaningful and successful if the mice are trained in the box successfully and if the box is able to take automated data.

Another aspect of a project's ending is to reflect on the project as a whole, its obstacles and its accomplishments.  Such reflections happen both internally in the scientist when considering what has happened in the project as well as externally through outlets like discussions in science papers.  To reach considering the project as a whole a prudent first step is to consider the various hurdles that took place.  In the behavior box experiment there were several challenges along the way.  The first major obstacle was in the research for the materials, in finding all the required parts with the correct dimensions and decent pricing.  The solution to this was patience and determination.  The second major challenge was the actual design for the port for the mice.  The issue was that none of the ports for the nose pokes that the lab had were large enough to allow all of the mice to poke through and set off the sensors.  Therefore, to solve this problem there was a brainstorming session and then the making of several ports.  After testing the ports and seeing the reactions of the test mice, some changes were made.  It was tested again a couple of times until the final port was decided on and then implemented.  The final major hurdle in this project was creating the ability for the ports to have the ability to be at two different distances from each other.  To solve this problem again there was brainstorming as well as making small prototypes of what was desired.  After some prototypes and discussions a layout was decided upon and that became the final model for the box.  Realizing such obstacles in research and taking the time to analyze both the challenges, solutions, and the processes to reach  a solution can help in future decision making for both the experiment and the scientist.  By using problem solving skills and critical thinking, both problems in the lab and out of the lab can be tackled and dealt with.

Another aspect of finishing research is the final days in the research lab.  This is a careful balance of continuing the research as well as working on the deliverables for the moment that the research project is finished.  Therefore, the last week is an amalgam between finishing up your project, organizing your area and materials, working on the presentations or posters or papers, and making sure that all of the work has been carefully documented.  The documentation and procedures are important to record because once one has left the lab there is still research and other projects being studied.  If one wrote a computer program and then did not tell anyone how it worked, if something needed to be changed or added the lab would have to try and figure out what the program involved or start over with a new program which would consume more time and energy than needed.  It is reasonable to expect one's final week then will be a lot of paperwork and the combinations of the research with how the research shall be presented.

It is important to use one's time wisely during this period because a lot of work and discussion takes place.  When writing up presentations, posters, and papers for research it is a discussion, a collaboration, and a cooperation with members of the lab both to check how the research is being presented as well as if the facts are portrayed properly as well as to catch any parts that need more clarification.  The purpose of sharing scientific research is so that others can either work collaboratively on joint research or can use information to enhance their own.  For either of these purposes however, communication is paramount to success where lucid and descriptive presentations are desired and necessary.  Research that is not understandable helps no one.

The BOX

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.

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.