Summer 2019
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Rules of Conduct
- No eating, drinking, or loud talking in the lab. Socialize in the lobby only.
- Be respectful to each other, regardless of level of study
- Be on time & responsible. Communicate in advance with the PI if late or absent
- No use of phone or laptop during lab meetings
Schedule
- June 19 (Wed). Summer research kickoff. Papers assigned. To prepare for Python tutorial, install the jupyter notebook in one of two following ways (by Edgar):
- Installing the Anaconda Distribution (https://www.anaconda.com/distribution/#download-section): This is the easiest way to install Python on your machine. It also comes with a lot of packages for data science. However, it is quite heavy (~3GB), so if space is an issue you can try installing Miniconda. If you choose to install Anaconda, you don't need to install any additional packages since they are going to be installed automatically. Make sure you download Python 3.
- Installing Miniconda3 (https://docs.conda.io/en/latest/miniconda.html): This is like a mini version of Anaconda that comes with the Conda package manager and Python. It doesn't include any packages so it requires less space.
- Installing on MacOs: https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html
- Installing on Windows: https://docs.conda.io/projects/conda/en/latest/user-guide/install/windows.html
- Once you install Miniconda, you can use the conda command on your terminal to install other packages:
conda install numpy
conda install pandas
conda install matplotlib
conda install jupyter
- June 21 (Fri). Python Tutorial I. Jupyter notebook, string, list, conditions, loops (by Edgar)
- June 24 (Mon). Python Tutorial II. string functions, function, dictionary, modules (by Edgar)
- June 26 (Wed). Python Tutorial III. BioPython (Edgar & Muhammud)
- June 27 (Thur). Paper presentations
Participants
- Dr Oliver Attie, Research Associate
- Brian Sulkow, Research Associate
- Saymon Akther, CUNY Graduate Center, EEB Program
- Lily Li, CUNY Graduate Center, EEB Program
- Christopher Panlasigui, Hunter Biology
- Summer Interns: Muhammad, Radhika Mohan, Oscar Eng, Oliver Cai
Journal Club
- a Unix & Perl tutorial
- A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
- A review on Borrelia genomics: https://www.ncbi.nlm.nih.gov/pubmed/24704760
- A model of immune selection: He et al (2018). https://www.nature.com/articles/s41467-018-04219-3
- A model of flu evolution: Neher et al (2016). https://www.pnas.org/content/113/12/E1701?ijkey=72c6025e999dd043d32f6822dc06c7356d8494b2&keytype2=tf_ipsecsha
- Reading on Dengue virus
Projects
| Project | Description/Goal | Participants | Leader | Header text |
|---|---|---|---|---|
| Lyme genomics | phylogeography & genome intragression | Saymon, Chris | Saymon | Example |
| Lyme ecology & population genetics | host identification; SIR model; coalescence | Lily, Chris | Lily | Example |
| Borrelia peptide library | Compile ORFs from genome database & send to Mt Sinai team | Chris, Saymon | Chris | Example |
| Origin of genetic code | manuscript revision | Oliver & Brian | Oliver | Example |
| Pseudomonas metabolomics | Shiny Web portal development | Chris, Edgar | Chris | Example |
| Dengue antigenic variations | Parse Dengue sequences | Oliver Cai, Muhammad, Che | Muhammad | Example |
| OspC design | Optimization by GA | Edgar, Lia | Brian | Example |
| OspC antigenecity model | Develop model with mice data by Invanova et al | Nevila, Brian | Brian | Example |
| OspC per-site model | Quantify per-site importance with likelihood, i.e., Prob{fit->0, given that CW50, site=i} | Radhika, Muhammad, Brian | Brian | Example |