Rich Lab:Useful Websites

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OSU Resources

OSU eMicro

• OSU Environmental Microbiology group
• Sequencing cost and options for our lab

Biophysics

• Data Science for Scientists Club
  • Data Science for Scientists Club is recruiting new members!
    • Open to any individual (students, postdocs or faculty) interested in developing skills necessary to analyze any type of data
    • No programming experience necessary! Club is a great place for absolute beginners to get introduced to the basics of data analysis and programming
    • Develop programming skills in Python, R and associated libraries
    • Share tips and tricks for data analysis and visualization
    • Email freitas.5@osu.edu or popova.4@osu.edu for more information
    • Meets every Tuesday 11:30am-1pm on Zoom ID https://go.osu.edu/datasci4sci_zoom
    • Attend our Zoom information session on Tuesday, March 23rd, Zoom ID https://go.osu.edu/datasci4sci_zoom at 11:30 am - 1 pm

Informatic & Microbiome Tools

Metagenomics Tools and Resources:

• Codes for SEPP, TIPP, UPP, HIPPI from the Warnow Lab at UIUC
  • SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
  • TIPP stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data.
  • UPP stands for "Ultra-large alignments using Phylogeny-aware Profiles", and addresses the problem of alignment of very large datasets, potentially containing fragmentary data. UPP can align datasets with up to 1,000,000 sequences.
  • HIPPI stands for "Highly Accurate Protein Family Classification with Ensembles of HMMs", and addresses the problem of classifying query sequences to protein families.
• MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. From the Doxey Lab at UWaterloo. Publication here.
• Metagenomic Intra-species Diversity Analysis System (MIDAS): An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. From the Pollard Lab at the Gladstone Institutes.
  • Open source software
  • Genomic database
• GREMLIN Metagenome Database
• MicrobeCensus estimates the average genome size of microbial communities from metagenomic data.
• CCoDA - Covariate-Corrected Dispersion Analysis. A test to identify significantly (in)variable gene families from count-based sequence data.
• phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
• BMC Bioinformatics
• Microbiome Analysis Tools Developed at EMBL: A web portal for computational microbiome analysis tools.

Proteomic Tools:

• Ben's spectra divvying Script
• SequenceServer
• Trans-Proteomic Pipeline (TPP)
• Scaffold Download
• Proteome Software: Scaffold Download
• PNNL MS Tools
• Software from the Tabb Lab
• The Global Proteome Machine: Tutorial
• The Chorus Project
• ProteoWizard
• Venn Diagram Plotter
• SignalP
• GLAMM - metabolic networks
• Instructions for installing and running DTASelect - Cravatt Lab
• Cytoscape KGML Reader
• Galaxy-P
• Proteomics with Galaxy
• Harvard's HutLab Tools for Microbial Datasets: A number of resources for metagenomic and functional genomic analyses, intended for research and academic use. Includes: Text manipulation, PICRUSt; GraPhlAn; MetaPhlAn; MetaPhlAn2; LEfSe; Filter and Sort; Join, Subtract and Group; Get Genomic Scores; MicroPITA; Extract Features; Phenotype Association. Plus NGS Toolbox (beta)

PROFESSIONAL DEVELOPMENT

• How to write a right cover letter when you submit a manuscript:
  • Cell Press, "Submitting your manuscript: Write the right cover letter"
  • Nature Methods blog, "How to write a cover letter"
  • Nature Chemistry blog, "50 ways to write a (cover) letter"
  • Springer, Cover letters"
  • Nature editor on how to write a rebuttal cover letter: [1]
  • Nature editor on how to write an appeal cover letter: [2]
  • One quite useful annotated template with tips - this is a great 1-stop-shopping place to dig in when it's time to write your letter: Wordvice's How to Write the Best Journal Submission Cover Letter
  • Another useful annotated template with tips: Publisher Taylor & Francis's recommendations
• Public Speaking:
  • TED talk, "Power Poses"
  • TED talk, "The Secret Structure of Great Talks"
• Navigating research life:
  • Six project-management tips for your PhD
  • The 11-step guide to running effective meetings
  • The Postbac: One or Two Years That Make Careers
  • How to manage up: Graduate students bear as much responsibility as their mentors for ensuring that they are well guided through their degrees, say Hugh Kearns and Maria Gardiner.
  • How to Talk to People, According to Terry Gross- the NPR host offers 8 spicy tips for having better conversations

Conferences & Workshops

• Symposium on Soil Metagenomics
• Terragenome Workshops, International Soil Metagenome Sequencing Consortium
• PNNL Events
• Pat Schloss' R workshop
  • Learn basics and some more advanced functions in R, focused largely on sequence data (recommended by Garrett).

Tutorials

• Lab techniques:
  • How to adjust the pH when creating media
  • How to operate a pH meter
  • How to pour plates
• Methods:
  • Illumina Sequencing Technology

Other helpful websites

• "Microbiomes in light of traits: A phylogenetic perspective". Paper discussing trait-based ecology
• GUSTA ME (GUide to STatistical Analysis in Microbial Ecology): An excellent primer and guide to ecological statistics
• MicroSeminar: Home of the Web-based Microbiology Seminar Series
• DNA Precipitation: Ethanol vs. Isopropanol: Article discussing the pros and cons of and the difference between precipitating DNA with ethanol vs. isopropanol and which is the better choice.
• United States Drought Monitor
• Sent to the lab by David Hogan, PhD student next door in the Maier Lab, an awesome database of useful Numbers and Sizes in Biology
• A great tool for choosing colors for figures in papers, presentations, etc.
• MIT Alumni Association
• How to make a good scientific poster?

PROFESSIONAL CERTIFICATES

• Ecological Society of America (ESA) Ecologist certification

WRITING TIPS

• A useful list of tips for science writing
• The 5 pivotal paragraphs in a paper

• Writing a rough draft of a scientific paper: expanding an outline until there's a paper

AUTHORSHIP GUIDELINES:

1. National Academies Press [On Being a Scientist: A Guide to Responsible Conduct in Research]
2. Nature Authorship Policies [[3]]
3. A Graduate Student’s Guide to Determining Authorship Credit and Authorship Order: http://www.apa.org/science/leadership/students/authorship-paper.pdf
4. PNAS authorship guidelines: http://www.pnas.org/content/101/29/10495.full

Other Cool Links

Glass microbe art by Luke Jerram