├── README.md ├── WeeklyReports └── WeeklyReportExample.md └── WritingCoverLetter ├── LICENSE ├── Michigan.pdf ├── README.md ├── Signature.pdf ├── cltemplate.tex ├── coverletter.md ├── coverletter.pdf └── renderletter /README.md: -------------------------------------------------------------------------------- 1 | # Lab Materials & Resources 2 | 3 | This repo is a small but hopefully useful collection of materials for labs. Check out the directories for more information, including templates. 4 | -------------------------------------------------------------------------------- /WeeklyReports/WeeklyReportExample.md: -------------------------------------------------------------------------------- 1 | # Report : 2016-04-29 2 | # Geof Hannigan 3 | 4 | ## Phage Purification for Phage Therapy 5 | 6 | I did some more phage hunting with Pat's animal fecal samples. Long story short, it was a bust and I did not get any phages again. From here I am taking two routes forward. 7 | 8 | 1. I tried emailing a few people to see whether I can get ahold of some purified phages to start getting some preliminary data with mice. As of now it looks like I will be able to get some E coli phages to use, which will be great. 9 | 10 | 2. I will be getting **sewage** from the **wastewater treatment plant** so that I can start isolating phages from it. I will start growing this both on E coli, as well as other bacterial hosts that are part of this list: 11 | 12 | * E. coli 13 | 14 | * Bacteroides fragilis 15 | 16 | * Bifidobacterium (genus) 17 | 18 | * Lachnospiraceae (family) 19 | 20 | * Barnesiella (genus) 21 | 22 | * Akkermansia (genus) 23 | 24 | ## Phage-Bacteria Interaction Prediction 25 | 26 | My script for predicting phage - bacteria associations using my protein network database is coming along nicely in my "down time". Right now I tried running it on my laptop because it is easier and I have the needed permissions, but I need to move it over to FLUX. Unfortunately I am having problems with the permissions so that is still a work in progress. 27 | 28 | ## Summary 29 | At this point it has been six months in the lab, which is terrifying because it means the year is half over and I need to make at least one paper happen before the end of the year. I think that these projects are the most likely to yield publications in both the short and long term. 30 | -------------------------------------------------------------------------------- /WritingCoverLetter/LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2017 Geoffrey Hannigan, PhD 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /WritingCoverLetter/Michigan.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Microbiology/Helpful_Lab_Materials/ae5f89a3a3d99189dde9409d3a308740947bc81e/WritingCoverLetter/Michigan.pdf -------------------------------------------------------------------------------- /WritingCoverLetter/README.md: -------------------------------------------------------------------------------- 1 | # PandocAcademicCoverLetter 2 | Easily write letters in your academic or other professional life. 3 | 4 | # Usage 5 | Create your letter by following the template provided by the example letter `coverletter.md`. You can change your signature and institute logo by changing the `Signature.pdf` and `Michigan.pdf` files, respectively. Once you have your markdown letter the way you like it, go ahead and run the shell script as: 6 | 7 | ```bash 8 | bash ./renderletter 9 | ``` 10 | 11 | See the final (example) product [here](https://github.com/Microbiology/PandocAcademicCoverLetter/blob/master/coverletter.pdf). 12 | 13 | # Dependencies 14 | This tool is pretty light on dependencies. All you need is to have Pandoc running on your computer. Don't yet have Pandoc? Follow the installation instructions [here](https://pandoc.org/installing.html). 15 | 16 | # Contributing 17 | Want to help fix a bug or add a feature? Feel free to submit a pull request. I also really value feedback from any users, so if you have an idea or a problem, please create an issue so that I can address it. 18 | -------------------------------------------------------------------------------- /WritingCoverLetter/Signature.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Microbiology/Helpful_Lab_Materials/ae5f89a3a3d99189dde9409d3a308740947bc81e/WritingCoverLetter/Signature.pdf -------------------------------------------------------------------------------- /WritingCoverLetter/cltemplate.tex: -------------------------------------------------------------------------------- 1 | %!TEX program = xelatex 2 | 3 | \documentclass[$size$]{letter} 4 | \usepackage[letterpaper,margin=1in]{geometry} 5 | 6 | \usepackage{fixltx2e} 7 | 8 | % Adds microtypography features: character protrusion, for XeTeX. 9 | \usepackage{microtype} 10 | 11 | % Allows links. 12 | \usepackage[usenames,dvipsnames]{color} 13 | \usepackage[xetex, bookmarks, colorlinks, breaklinks]{hyperref} 14 | \hypersetup{colorlinks=true, urlcolor=NavyBlue, linkcolor=NavyBlue} 15 | 16 | \urlstyle{rm} 17 | 18 | \frenchspacing{} % Remove extra spaces after periods. 19 | \pagestyle{empty} % Remove page numbers. 20 | 21 | \usepackage{fontspec} 22 | \defaultfontfeatures{Mapping=tex-text} % Sets quotation marks. 23 | \setromanfont{Times} 24 | \setsansfont[BoldFont={Helvetica Neue Bold}]{Helvetica Neue} 25 | \setmonofont[Scale=MatchLowercase]{Helvetica} 26 | 27 | % From default template 28 | \providecommand{\tightlist}{% 29 | \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} 30 | 31 | \newcommand\shyp{\-} 32 | 33 | \newcommand{\header}[9]{ 34 | {\hypersetup{hidelinks} 35 | \noindent 36 | \parbox[b][0.625in][t]{6.5in}{ 37 | \vspace{-0.375in} 38 | \parbox[b][0.625in][t]{3.74in} 39 | {\href{http://www.umich.edu} 40 | {\includegraphics[height=1in]{./Michigan.pdf}}}\hfill 41 | \parbox[b][0.625in][t]{2in}{ 42 | \setlength{\baselineskip}{9pt} 43 | \fontsize{7pt}{7pt}{ 44 | \fontspec{Helvetica} 45 | \textbf{#8}\\ 46 | {#9}\vspace{6pt}\\ 47 | #1\\ 48 | #2, #3 #4\\ 49 | Phone: #5\\ 50 | Fax: #6\\ 51 | Email: \href{mailto:#7}{#7} 52 | } 53 | } 54 | }} 55 | } 56 | 57 | $if(draft)$ 58 | \usepackage{draftwatermark} 59 | \SetWatermarkLightness{0.9} 60 | $endif$ 61 | 62 | \begin{document} 63 | 64 | \header{$head.address$}{$head.city$}{$head.state$}{$head.zip$}{$head.phone$}{$head.fax$}{$head.email$}{$sig.name$}{$head.dept$} 65 | 66 | 67 | \vspace{0.5in} 68 | 69 | $body$ 70 | 71 | $if(sig.include)$ 72 | \begin{minipage}[t]{6.5in} 73 | Sincerely,\\ 74 | 75 | \vspace{0.1in} 76 | 77 | $if(sig.sign)$ 78 | \vspace{-0.2in}\includegraphics[height=0.5in]{./Signature.pdf} 79 | $else$ 80 | \\ 81 | $endif$ 82 | \\ 83 | $sig.name$\\ 84 | $sig.post$ 85 | $if(sig.secondpost)$ 86 | \\ 87 | $sig.secondpost$ 88 | $endif$ 89 | \end{minipage} 90 | $endif$ 91 | 92 | $if(cc)$ 93 | cc: $for(cc)$$cc$$sep$, $endfor$ 94 | $endif$ 95 | 96 | $if(ps)$ 97 | $ps$ 98 | $endif$ 99 | 100 | \end{document} -------------------------------------------------------------------------------- /WritingCoverLetter/coverletter.md: -------------------------------------------------------------------------------- 1 | --- 2 | size: 11pt 3 | draft: no 4 | head: 5 | address: '123 Research Ave, Science Building 2' 6 | city: Cambridge 7 | state: MA 8 | zip: 02114 9 | phone: '\(121\) 555-2234' 10 | fax: '\(999\) 555-6565' 11 | email: 'hannigan@gmail.com' 12 | dept: "Microbiology & Bioinformatics" 13 | sig: 14 | include: yes 15 | sign: yes 16 | name: 'Geoffrey Hannigan, PhD' 17 | post: Bioinformatics Scientist 18 | secondpost: Distinguished Second Appointment 19 | --- 20 | 21 | \today 22 | 23 | 24 | To the editors of Science: 25 | 26 | We submit for your review: "The role of the microbiome in health and disease" by Geoffrey Hannigan and colleagues. We believe this work to be especially well suited for publication in Science and highly relevant to a broader scientific readership as well as the general public. 27 | 28 | Our lab strives to set high standards of reproducibility and transparency, while generating and publishing high quality data. As such, all analysis work-flows, scripts, and datasets have been made publicly available for other researchers to utilize. 29 | 30 | The data presented in this manuscript are original and the manuscript is not under consideration elsewhere. A preprint version of this manuscript has been made available through BioRxiv. 31 | 32 | We thank you for your consideration and look forward to your response. 33 | -------------------------------------------------------------------------------- /WritingCoverLetter/coverletter.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Microbiology/Helpful_Lab_Materials/ae5f89a3a3d99189dde9409d3a308740947bc81e/WritingCoverLetter/coverletter.pdf -------------------------------------------------------------------------------- /WritingCoverLetter/renderletter: -------------------------------------------------------------------------------- 1 | #! /bin/bash 2 | 3 | echo Running Pandoc... 4 | pandoc \ 5 | --latex-engine=xelatex \ 6 | --template=cltemplate.tex \ 7 | -s ./coverletter.md \ 8 | -f markdown \ 9 | -t latex \ 10 | -o ./coverletter.pdf 11 | echo Done 12 | --------------------------------------------------------------------------------