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Summer Research Experience: Student Blog

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Improving Forest Change Modeling, One Parameter at a Time

August 2, 2016, by Patrick McKenzie
Alongside uncertainty about the stability of future climate conditions comes uncertainty about future landscapes: Where will our forests be in 200 years? Forest landscape models have been designed to address this. Forest landscape models take small-scale ecological phenomena and apply them across large spatial and/or temporal scales. LANDIS-II (“LANdscape DIsturbance and Succession”) is a forest landscape model that consists of a core program with several extensions that are downloaded separately and can be individually activated to simulate various ecological processes. Together with its...Read more >

Dealing with (Computer) Bugs in the Forest

July 28, 2016, by Moe Pwint Phyu
Imagine you are a scientist with amazing data sets trying to make a groundbreaking discovery. But first, you need to replicate the way that an earlier scientist analyzed data sets for you to contextualize the experiment. And you painstakingly replicate every step of the whole analysis, but then you run into bug after bug in your code. You finally figure out that you missed a crucial step in the data manipulations leading up to the statistical tests—because the earlier scientist forgot to mention it in their methods. My mentors, Barbara Lerner and Emery Boose, try to tackle this problem by...Read more >

Data is Eating Ecology: How We Make Sense of It

July 19, 2016, by Siqing "Alex" Liu
Marc Andreessen famously proclaimed that “software is eating the world,” and to me, data is certainly eating up ecology. Andreessen meant that software is fundamentally changing how companies and economies work, and that the incumbents will be taken over by software companies. Though not a direct analogy, data is changing ecology by impacting every stage of the scientific enterprise, from hypothesis formation to conclusion. This explosion of data comes from multiple sources, from the proliferation of cheap sensors to the better detail and scope of satellite coverage. This flood of data has...Read more >

Coding the Future (of Ants)

July 8, 2016, by Anna Calderon
What if you could see into the future? Perhaps you are interested in knowing where your favorite animal or plant may be located fifty or one hundred years from now. It might be difficult to imagine what the world would look like, but species distribution models attempt to do just that. A species distribution model (SDM) is a method used to produce maps that attempt to predict where a species might occur in the future based on environmental factors that govern its current location. SDMs are powerful tools which have a wide range of applications: for conservation purposes, to predict where...Read more >

How to roll your R’s like a scientist! / Aprendiendo la R científica

August 2, 2015, by Mayra Rodríguez-González
[The English version of this post is followed by a Spanish version, also written by Mayra.] In a world where both natural and human driven disturbances have caused an array of changes in the landscape, we would expect that land-use and land-cover change could become either an asset or a threat to our environment. Here at the Harvard Forest the landscape simulation crew has joined forces to predict land-use change effects on the ecosystem and its services. These services are benefits obtained from ecosystems that provide people with necessities such as fresh water, food and fuel. Understanding...Read more >

Ecological Tipping Points and Warning Signs

July 30, 2015, by Nathan Justice
It takes a very special kind of person to be an ecologist. They must be tenacious, inquisitive, and most importantly, they must demonstrate unyielding optimism. A common goal amongst ecological scientists is to better understand the world around us, and to capitalize on this knowledge in order to facilitate Nature's narrative with minimal human interruption. Ecology, along with sibling-branches like conservation biology, wildlife biology, and forestry, have a tendency to feel like an uphill battle in pursuit of this goal. Despite the appearance of ecological processes progressing at a...Read more >

Creating A New England Forest Map

June 6, 2014, by Sofie McComb
Matthew Duveneck and Sofie McComb analyzing data in the scripting language R
The first week at Harvard Forest has passed and it already feels like I have been here for a month. There is always so much going on and so many things happening that time just flies by. Orientation was a two day whirlwind and finally on day three all the students got to meet their mentors and get to work. I am working over the summer with my mentor Matthew Duveneck, who is a post doc working with Dr. Jonathan Thompson, who is my advising professor. The project I am working on with them is the creation of a map of the New England Forest based on satellite image data, data collected by...Read more >

Debugging Ecological Research

June 6, 2014, by Luis Perez
Barbara Lerner, Luis Perez, Nikki Hoffler, and Emery Boose working
With ecology, as with an increasing number of other fields, "big data" has become an intrinsic aspect of scientific research. Ask most field scientists and, with a grunt of disapproval mixed with displeasure, you are likely to hear about all the programming and statistical analysis that has to be done to gain meaningful results. Consider t he inevitable sensor drift that occurs and the recalibration that must take place to restore validity to the data; or, imagine a flash flood, lighting strike, or simple technical failure that can lead to incorrect or unavailable sensor readings. As larger...Read more >

You down with DDG?

August 2, 2013, by Shaylyn Adams
Shaylyn Adams and Vasco Carinhas
"Ooh you're working at the Harvard Forest, that's cool, right?! You get to swing from trees, work on your tan, get some exercise and play with chipmunks, right?!" Well, actually, wrong (and I'm sure most field work is not that glorious). Instead of building tree forts and befriending Bambi, my job at the Harvard Forest takes place pretty much completely inside (and with the deer flies this season, that's the way I like it). Not that I don't sweat; it gets fairly hot inside the Shaler building dining hall where there is no central AC. Nevertheless, rain or shine you can always find me and my...Read more >

A thousand little blank puzzle pieces

July 30, 2013, by Lake Boddicker
One of the aerial tram's sensors.
For the past two months I have been working on building an aerial tram with my two great teammates Devin Carroll and Faith Neff. This consisted of me sitting in front of a computer, occasionally graced by the presence of a sensor and motor, wondering why nothing was working. I think that I have gotten more of a tan from the computer screen than the actual sun. As I so found out, however, things did work, just slowly. But bit-by-bit, piece-by-piece things came together like a thousand little blank puzzle pieces. The first piece of the puzzle that started to work was the data logger. This was...Read more >

Exit the matrix

July 26, 2013, by Vasco A. Carinhas
There is life outside the Matrix. We, as computer scientists, sometimes tend to forget that. However, Harvard Forest makes sure we are reminded on a daily basis. Besides our trampling through the fascinating virtual world that is created through coding, we are thrust into the world that already surrounds us as part of our summer internship experience. One of our duties includes exploring the field in order to collect the saved data from the six hydrological stations distributed along the brooks and swamps in the vicinities of Prospect Hill. So, weekly, armed with a palm-pilot, a data sheet,...Read more >

Let's build a robot!

June 14, 2013, by Devin Carroll
Image courtesy of
When people hear the word robot they probably think of something like the photo below, a humanoid machine that acts like a person, but is smarter and stronger in nearly every way; robots that are self-aware and may be preparing to rise up against their creators. The primary goal of the robots from the above picture is to help people. Everything they do, every action they take, is intended to make their caretaker's life easier. It's important to note, that in today's world, every robot we have built was designed with the intention to make someone's life easier and safer. Whether they are the...Read more >

Trees and bugs in computers

August 10, 2012, by Yujia Zhou
Scientists often rely on sensors to collect data. However, sensors can go wrong due to various surprising yet possible reasons. Have you ever thought, what you would do if you lost a couple of hours’ data because a lightning destroyed the sensor? Also, your sensor may freeze during winter time due to low temperature. Moreover, certain sensors require calibration every year because of inexorable sensor drift. As a result, raw data is usually not very reliable before some special processing, or “quality control.” This summer, I worked with Dr. Emery Boose and Prof. Barbara Lerner on quality...Read more >

Visualization tools for digital dataset derivation graphs

August 10, 2012, by Miruna Oprescu
If you were a scientist working with more than 10,000 new data points every week, how well would you be able to keep track of all the changes you made to the data to obtain the final results? Moreover, if you were to look at your research 5 to 10 years from now, how well would you or any other scientist be able to reproduce your results from the original data? This summer, I am working with Emery Boose, researcher at Harvard Forest, Barbara Lerner, professor of Computer Science at Mt. Holyoke College and Yujia Zhou, rising senior at Dikinson College, to develop effective tools for creating,...Read more >

Global warming and forest soil micro biomes

July 19, 2012, by Sonia Filipczak
Global Warming has become a topic under much debate, yet carrying implications that affect everyone. Whether you are young or old, plant, animal, or microbe, some of the obvious signs such as less snow in the winter and unbearably hot summers should remind us how much of an impact each individual has on our world. Among all of the individuals on this planet, soil microbes make up a large population and their response to climate change should be of concern. After all, there are more microbes in a teaspoon of soil than people on Earth! Similar to us, microbial communities are affected by the...Read more >

REUs ace summer symposium!

August 12, 2010, by Aleta Wiley
In the final week of the Summer Research Program in Ecology for Undergraduates at Harvard Forest, all 33 students participated in the Student Symposium on August 11-12 in the Fisher Museum. Over a day and a half, all the students presented 15 minute talks to an audience comprising program mentors, university professors, Harvard Forest researchers, family members, and of course, their fellow students. As each student discussed his/her summer research, the audience was impressed with the diversity of projects presented ( Abstracts are available here ). Since Harvard Forest is an LTER (Long Term...Read more >

Using models to project how climate change might affect oak species distribution

August 10, 2010, by Elisabete (Baker) Vail
Imagine if crystal balls which allowed us to catch a glimpse of the future, actually existed? What would you use them to see? Well, in a way – they do exist. In the abstract world of math and computers, “models” are fed datasets of current day information and asked to project future outcomes. Ecologists use them to forecast how current events will shape our future planet. This is what I have spent my summer, attempting to do. My project attempts to project the possible affects that increasing climate change may have on oak species distribution. Focusing on 27 oak species, located across the...Read more >

Using computer science at Harvard Forest to increase integrity of scientific conclusions

August 3, 2010, by Sofiya Taskova and Morgan Vigil
This summer, we have had the privilege of working with Dr. Emery Boose and Dr. Barbara Lerner on a project involving a mash up of ecology and technology. For the past few weeks, we have been inundated with the buzzwords "data provenance", "sensor network", "Process Derivation Graphs", "Data Derivation Graphs", "stream discharge", and "weirs". Our headquarters is located in the Shaler Common room (where we do most of our programming and computer work), but we do make a weekly trip out to the six hydrology sites in the forest to collect manual and logged data as well as water samples and...Read more >