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BridgeUP-STEM-Xiao

This is the GitHub repository for Madelyne Xiao's 2018 - 2019 BridgeUP:STEM internship group

This is the home of #coralcrew's internship code and projects. By the end of the internship, we will have :

  • written data cleaning, analysis, and visualization scripts for mitogenome data
  • gained a deeper understanding of black coral and anemone phylogenies
  • built some phylogenetic trees of our own!

Jot down some of your own goals here:

Below, you'll find a week-by-week breakdown of our work.

Week 18: Beginning Data Visualization

  • Reviewing Python Pandas dataframes
  • Getting our feet wet with some sunspot data! Graphing and binning datapoints.

Week 17: ATCG Analysis

  • AT and GC skew analysis for leading/lagging strand identification
  • purine and pyrimidine skew analysis for heavy/light strand identification

Week 16: Visualizing Genomes

  • building our own DNA walk visualizers using Python's tk package

Week 15: Phylogenetics in the Wild

  • finishing translations of our data files
  • exploring some well-known phylogenetics concepts, as found in the museum!
  • a talk with Dr. Nathalie Goodkin, a marine chemist in Earth and Planetary Sciences

Week 14: Genetic Codes and Translation

  • learning about different types of genetic codes
  • translating our raw nucleotide data files using Python dictionaries

Week 13: The Whole Pipeline

  • reviewing the pipeline we've built over the past three months, from raw data to tree
  • starting an exploratory data analysis of our raw FASTA files

Week 12: New Year, New Tree

  • Learning about the variety of tree-drawing methods available
  • Using Phylip to build some phylogenetic trees from our distance matrix input files

Week 11: Presentations and break

  • presentations -- great job, coral crew!

Week 10: More Alignment and Distance Matrices

  • creating input files for tree construction!
  • preparing for next week's mid-year presentation

Week 9: More Alignment and Distance Matrices

  • building distance matrices from alignment files (and, from distance matrices, building trees!)
  • start thinking about Dec. 20 mid-year presentations

Week 8: Finishing Assembly, More Alignment

  • we'll present our solutions to the assembly algorithm (at long last!)
  • more work on BLAST with Biopython, intro to distance matrices

Week 7: Meeting Mercer

  • short week -- on Tuesday, we spoke to Mercer about his research and got a tour of the wet collections -- saw a giant squid, a giant aquatic isopod!

Week 6: Assembly cont'd, beginning Alignment

  • made our own DeBruijn graphs with texts of our choice!
  • learned about the bridges of Konigsberg problem and Eulerian walks
  • began working with BLAST for sequence lookups

Week 5: Assembly Algorithms (short week)

  • on Thursday, worked on writing our own brute-force algorithms to align two nucleotide contigs.
  • also discussed big-O notation, algorithmic efficiency, and some common algorithmic problems (e.g., sorting, traveling salesman)

Week 4: Genomes, Assemble!

  • discussed the process of genome assembly through a hands-on 'assembly' of familiar and less-familiar sets of song lyrics (context is important!)
  • tried our hand at building trees with a candy phylogeny (happy Halloween!)

Week 3: Data Cleaning

  • began writing our own functions to solve the noisy data problems we encountered last week

Week 2: DNA Detectives

  • learned about some common features of noisy biological data
  • intro to a new Python package, BioPython!

Week 1: Github Essentials

  • played a collaborative story-writing game called Exquisite Corpse to practice git pulling, pushing, and text-editing on the command line
  • learned some nifty new Unix commands and shortcuts!

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