Here is the tutorial for the total-evidence divergence time tutorial.
Here are the code files.
And here are the data files.
Slides to be posted.
I’m out at Bodega Bay Marine lab for the 2017 Applied Phylogenetics Workshop. I’ll be talking about some of the work Walker Pett, undergraduates Andre Flores and Pat Mendoza, and I have been doing on morphological character change models. Slides for my tutorial are here, code and data are here, and I’ll post lecture slides Thursday.
Editor’s Note: Every semester, we bring on new undergraduate researchers to the project. We do a lot of basic-level training for computational biology. If you’d like to follow along at home, our schedule is here.
I’m Andre, an undergraduate studying both Biology and Computer Science. I intend to pursue a medical degree in the future, hopefully incorporating bioinformatics to work in the fields relating to psychology and neuroscience. Working in the Heath Lab is my first experience working in a real research environment, an integral part of preparing my resume for graduate school. Furthermore, the lab is my first real opportunity for combined education and hands-on experience between my two drastically different areas of study. I’m hoping to learn a lot more programming skills and knowledge about phylogenetics, and the ways in which they can work together to study biology.
I am a student majoring in Horticulture with an anticipated graduation in Spring ’18. I’m coming to Ames after working in financial analysis for 13 years and with an existing BS in Mathematics, specializing in Statistics, from the University of California Irvine. This semester I hope to expand on my skill sets as a programmer learning python and R as well as the application of statistics to further scientific research. My interests are in mutualisms between plant and animal as well as mycorrhizae and phylogenies. In the fall I will be applying to grad programs with the intent of pursuing a career in research.
The Paleantology project was at the Society of Systematic Biologists standalone meeting this week. Below are the slides for my talk. If you want to try the model discussed, there is a use-case in the Total Evidence Dating RevBayes tutorial given by Tracy Heath, Walker (Will) Pett and myself. Feel free to get in touch with questions, or for help implementing the model with your own data.
Will and I have a couple students starting with us this week to elucidate aspects of the performance of the model discussed. Watch this space to get to know our students and their project!
Project PI April Wright (yours truly) and project sponsoring scientist Tracy Heath will be at the Society of Systematic Biologists standalone meeting Jan. 6 – 11 in Baton Rouge. Both of us will be involved in the RevBayes workshops over the weekend. My lightning talk will be Tuesday at 3:40. Watch this space for links to the finalized slides and tutorial materials.
And if you’re around, make sure to come say helleaux!
Editor’s Note: We’re finishing up our first semester of the Paleantology project! One big problem to managing big data is making sure you’re able to organize everything, and make that data accessible. I wrote a little about that here. Another issue is making sure data are entered without error. To that end, Krishna Gandikota joined the lab for the fall to learn more about programming. He worked on creating a software to automatically download and parse taxonomy information for the ants in our dataset. He’s leaving us for the University of Iowa biomedical engineering program. He worked with me on a piece of software to parse ant taxonomy information from AntWiki. Good luck in Iowa City, Krishna!
What does the software you worked on in the lab do?
The software that we created downloads taxonomy data for the ants in the fossil and molecular datasets. It reads a txt file containing the names of taxa, and converts them into urls for the AntWiki database. The urls are stored in a dictionary structure. Furthermore, it makes an http request to a URL and then uses Beautiful Soup and regular expressions to get specific information from the webpage. The last step of the program consists of writing out the new ant data to our ant taxonomy database.
What have you learned?
Initially I thought python could be used for writing normal code. Through this project, I learned that python has more capabilities for scripting and making http requests. The language is easy to handle and is much simpler than the other languages I have been exposed to. Overall my experience with the project as well as the language was beneficial.
What do you still need to learn?
The skills I need to develop include the ability to discern the structure of a function I want to create, including performance tuning. I need to learn how to code without making syntax errors. Memorizing the basic functions and syntaxes will make the coding process more efficient, and will come with more practice.
Paleantology postdoc April Wright wrote a short piece for the Data Carpentry website on developing and maintaining resources for biologists to learn about programming and data management. Data Carpentry is always looking for learners, mentors and project maintainers, so head on over to find out how you can play a role in this community!