This document provides guidance for Computational Biology majors and their advisors. Information on the major in Biology is available separately. From the college catalog: The major in computational biology allows students to develop a coherent plan for the integration of computer science with biology. Students completing this major will be well prepared to obtain employment or pursue research in fields such as computational biology and bioinformatics. Major requirements Students will design an integrative course of study in collaboration with academic advisors from the Biology and Computer Science departments. It is each student's responsibility to make sure they meet major requirements. Faculty act as advisors only.

This document provides guidance for Biology majors and their advisors. Updated 13 December 2023, for classes matriculating Fall 2020 and onwards. Information on the major in Computational Biology is available separately. It is each student's responsibility to make sure they meet major requirements. Faculty act as advisors only. Major requirements [ ] 31 total credit hours* in Biology (BI or cross-listed BC, ES, SC, etc.) [ ] BI163 The Cellular Basis of Life and BI164 Evolution and Diversity; or BI201 Biology Accelerator [ ] A field biology course with lab: BI211, BI237, BI241, BI253, BI254, BI271, BI277, BI334, BI373 (if taken with lab), BI384 [ ] A cell biology course with lab: BI215, BI225, BI227, BI248, BI274, BI279, BI347, BI351, BC367 [ ] Six biology courses with labs*


October 20, 2021 - Dave Angelini Should you get a vaccine to protect yourself from Covid-19? Should you vaccinate your kids? :::warning The simple answer to these questions is, yes. Without reservations and unequivocally. (Summary figure) ::: To understand the reasoning behind this conclusion, please read on.

Students in the Biology Department gain exposure to the breadth of biological sciences and become skilled in the methods of scientific inquiry. The curriculum emphasizes the study of plants, animals, and microorganisms from the molecular to the ecosystem level. Research is integral to our teaching and learning. Biology majors work closely with professors to generate hypotheses and conduct self-designed experiments. Major in Biology The Biology major is flexible, allowing students to develop a course of study matching their particular interests. We offer concentrations in cell and molecular biology/biochemistry, neuroscience, and ecology and evolution. Biology major requirements Major in Computational Biology The major in computational biology allows students to develop a coherent plan for the integration of computer science with biology. Students completing this major will be well prepared to obtain employment or pursue research in fields such as computational biology and bioinformatics.

BI376 For the week of 14 September 2020 Rmd version of this script Tutorial instructions The final project for BI376 this semester will employ morphometric analysis in R, a free platform for statistical computing. While you've probably encountered R in other courses, this tutorial is meant as a refresher and as a reference. Later lab protocols will provide information on how you can explore more advanced features. While I hope you will look through all of this document, some of the material may be familiar and some may be new. At the end, there is a brief exercise asking you to send in a demonstration of your R skills.

Link to untested Bread Ideas :::info General tips Start the yeast. For any recipe using dry yeast, mix the yeast with warm water (110-115˚F) and about 1 teaspoon of honey. Let it stand for 5-10 min, until foamy. This will activate the yeast. In any recipe, it's possible to substitute sourdough starter for flour and water. For example 100 g of starter can replace 50 g water and 50 g flour. Be sure to keep at least 50 g of water in the recipt to start the yeast-- and it does seem wise to keep at least some dried yeast in the bake. In our convection oven, it's always necessary to cover bread to prevent the top from burning. Place a bread pan in the air frying basket on the bottom rung to maximize its head space. :::

27 November 2022 Based on BLAST of transcripts from the Reed & Pillardy transcriptome to the chromosome-level NCBI VanCard 2.2 genome assembly. Sex determination genes vermilion chr19, plus strand 8 exons The second of our sgRNAs, T7-Vc-v-618-Cas9sg, targets a polymorphic site.

Resources A reference on proofing. Twisted Black Forest Bread My own invention. But based on Mark Bittman's sandwich bread recipe. Ingredients Prepare two seperate doughs

Caseless turkey “sausage” 1 lbs ground turkey ¼ C parsley, dried 2 Tbsp fennel seed, freshly crushed 1 clove garlic, minced 1 tsp black pepper ½ tsp sea salt ¼ tsp celery salt Mix everything. Cook like it was sausage.

The tutorial is available here. Practice Problems Each of the questions applies to the file /export/groups/drangeli/rnaseq.sample.fq Start by copying it to your home directory. Problem B1 How frequent is the EcoRI recognition sequence, GAATTC?

This is a lesson plan to teach basic commands to new users of the bash command line. For other resources, check out Software Carpentry. Bash basics Bash is a Unix or Linux shell. You can think or it as a local dialect of Linux. There are some small differences in syntax compared to other shells, such as tsch. Take notes! Note taking is important! Just like you'd keep a lab notebook at the bench, if you're working at the terminal, you should keep detailed records of what you've done and explanatory notes to yourself. There are lots of ways you could do this, including using a paper notebook, Word, Google Docs, or a text editor. I recommend taking notes in Markdown format, a simple way to annotate your notes in a text document. The major advantage to Markdown over something like Google Docs is that it is fundamentally just text, and it can be easily moved to new platforms. Most of our workflows will end up in Rstudio where Markdown code can seemlessly become Rmarkdown code. In this way, your entire workflow, from bash to R, can be recorded in one simple document. You can write Markdown easily in any plain text editor. My favorite is Atom. However, you may want to use an editor that is specialize for Markdown. Several excellent free options exist.

Thanks for watching Kousa & Clem! Feed them twice a day, morning and evening. They are not particular about exactly when. Dry dog food is in the large white plastic tub opposite the wall clock Wet dog food cans are in the garage, at the end of the desk on the right as you enter from the kitchen. Clem a scant cup (about 225 ml) of dry food a spoonful of wet food

This document describes how to run command-line BLAST with custom search-able databases on Colby's nscc. Running BLAST on nscc "BLAST+" is a suite of linux programs that run the different variations of the basic local alignment search tool (BLAST) algorithm. It can be run on n26 (the Biology node). Which program you need to run (blastn, blastp, blastx or tblastn) depends to whether your search query is a nucleotide or amino acid (protein) sequence and whether you're searching a database of nucleotide or protein sequences. Once you know the variety of BLAST you need, the basic form of the command is: blastn -query /path/input.filename.fa -db /path/BLASTdb > output.filename Notice that the default is for BLAST to send its output to "stdout", that is, the screen. So typically you want to redirect that output to a named file.

Hi everyone, I haven’t yet posted pictures form our Costa Rica trip to Facebook. I’m hoping to do that at some point soon. But being an obsessive bio nerd I’ve posted my animal and plant photos to the citizen science site iNaturalist. Not all the photos are great, but some are worth looking at. Below are links to particular creatures by group. Cheers, Dave For pages that list multiple sightings, click in the thumbnail image for a larger picture. Everything!

Link to Bread Notes Link to Bread Ideas Oatmeal Granola Bread 21 November 2020 milk 1C salt 1/2 tsp butter 2 Tbsp oatmeal 3/8 C

Dave Angelini, 14 May 2021. GenBank is a vast open access collection of all available nucleotide sequences maintained by the National Center for Biotechnology Information (NCBI). Every time I need to submit sequences to GenBank, typically before submitting a manuscript for publication, I struggle to remember how best to do it. There are many tools, and none of them ever seem to fit what I'd like to do. This tutorial is meant to serve as a record of one successful and relatively painless workflow. Clean up the sequences. Create a folder in Geneious that contains all of the sequences to be submitted for a particular project. Annotations should be limited. GenBank only requires annotations for CDS. The gene annotation is required only if the sequence contains multiple genes, but is reccomended for all submissions. If they are known, exon annotations should also be included. CDS annotations must have two properties: transl_table with value 1 (for the universal genetic code), and codon_start with value 1 (assuming that the start codon is included, otherwise this value should be the reading frame). exon annotations must include the property number with numerical value indicating the exon's number.

:::warning Conclusion: Vote No on Question 1 to prevent 3.5 to 4.1 megatons of net CO~2~ emissions annually, at the cost of 963 acres (1.5 square-miles) of forest. ::: Motives I am put-off by the fear-mongering, xenophobia, and green-washing from all sides of this issue. As a voter, I concerned with longterm environmental preservation. I am willing to sacrifice some natural areas, if it means broader protections for the environment, and I'm not motivated by "not-in-my-backyard" complaints. That means the terms of comparison here are in units of electricity production and consumption and carbon production and sequestration. Question 1

Please redirect to https://hackmd.io/@EcoEvoDevoLab/AngeliniLab 

EcoEvoDevo Lab By Victuallers - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=35119980 Measuring concentration and DNA storage Use the NanoDrop spec to measure the concentration of DNA. Record this information in your notebook and on the side of the tube. Also note the purity of the sample. Pure DNA should have an A260/A280 ratio ~ 1.8 and an A260/A230 ratio > 1.8 Store DNA at 4˚C for less than a week or at -20˚C for longer periods. PCR purification