Open Science

Configuring git

Creating an ssh key and adding it to our authenticator To check if we have an ssh authentication already we run on the terminal: ssh -v If we have the ssh authentication we will a message like this: Hi User Name! You've successfully authenticated, but GitHub does not provide shell access. If it is not succesful, follow to the next section. Generate the key We will write the following command by replacing the email within quotations with the email we used to sign up on github.

Scientific writing Workshop

From Carrie Kouadio Links from Dr. Tiffany Vora Workshop outline: Exercises: ProTips: Before You Start Writing:

Syllabus development

Course: Data science research in biology Course learning outcomes: Experience the process of scientific discovery, including the iterative nature of biological research. This includes: discover and formulate their own scientific questions with clear, testable hypotheses. draw conclusions from analysis of novel data apply background knowledge to develop and interpret their research Engage in highly collaborative research teams to carry out a scientific research project Learn common scientific practices employed by biologists, including common tools, instruments, and software Communicate their research and discoveries at both technical and non-technical levels These are the CLOs for BIO 197: Culminating Experience CLO 1.

Guidelines for authorship

Co-authorship Guidelines: Providing written content to outline, manuscript, figures, tables, or substantial edits to the manuscript. Authorship order - For middle authors that contributed equally, assign order by random number generator. Indicate contributor roles to the project using CRediT Taxonomy (Contributor Roles Taxonomy ( Providing/confirming affiliation prior to manuscript submission within approx 2 weeks of being notified. Endorsing final content of manuscript within given approx 2 weeks of being notified.

Physcraper Demo

Background: What is a phylogeny and why is it the hot stuff in Biology. Making a phylogeny. Getting genetic data. By yourself! From public databases, Genbank Getting a starting homology hypothesis. Construct your own! Get one from TreeBASE Getting a published genetic tree. Google scholar OpenTree Physcraper:


Review of reproducibility concepts and advancement in biological science. Homework for sortee github hackathon September meeting. «Last month we discussed each finding and briefly summarizing 2 articles/white papers/books/blog posts on GitHub. If you are able to locate articles and summarize them, please add them to the list that starts on page 2 of this google doc:" Documentation is a key aspect for replication and reproducibility:

Jan 21, 2021

Today I’m trying to install Physcraper in a new computer, a 2015 MacBook Air. The goal is to check for installation issues The computer still has python 2 as default. How to make python 3 the default? We worked on a bunch of issues from documentation, on a separate branch. At the same time, EJM fixed errors on main branch and to merg main into our working branch I did

laTeX issue with rmarkdown's render

It’s 8pm in Merced, California, beginning of fall and we’re 35C. I’m working on job applications and I’m trying to render a document written in R markdown to word and pdf documents. The method I always use is suddenly failing while trying to render my Rmd file to pdf. When rendering via RStudio, pressing the render button from the research2pdf.Rmd file, the process just gets stuck, so I switch to a terminal to run R from the command line.

Physcraper: A Python package for continual update of evolutionary estimates using the Open Tree of Life

In this paper we present Physcraper, a Python package for update of phylogenetic relationships using existing expert-curated alignments and molecular data from GenBank that has not been analyzed in an evolutionary context yet.

Open Science and Reproducibility

Go to [presentation.](