Running a job on a cluster If you are outside the cluster network, turn your VPN on! For security, on most cluster you can only ssh into them from within their network. If you are working from outside the cluster network, for example, from home, you will have to start a VPN to connect from within the cluster network.
ssh into the cluster ssh USER-NAME@CLUSTER.ADDRESS Create a job submission script.
From Carrie Kouadio
Links from Dr. Tiffany Vora
Workshop outline: https://drive.google.com/file/d/1gV9vEwR7UgWl0Yxi7NRc4JoSxFiJVuWl/view?usp=sharing
Exercises: https://drive.google.com/file/d/1zyGFI8oaFjdR0ZJ4TWMC1T-H-MO_1qw2/view?usp=sharing
ProTips: https://drive.google.com/file/d/14YmInJ8TlYeFN1qjuVgSiY5vVyBShhnV/view?usp=sharing
Before You Start Writing: https://drive.google.com/file/d/1JPq35Y3mWeWsT0VM_YZAdJcJ-niPx9vI/view?usp=sharing
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.
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 (https://casrai.org/credit/). 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.
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: https://docs.google.com/document/d/1xQ8Ol5_a4di64zip228UtJHzneSSCyEvmQ1mP2JG47E/edit#" Documentation is a key aspect for replication and reproducibility: