Rich Lab:Useful Websites
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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.
- 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.
- Ben's spectra divvying Script
- 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
- Venn Diagram Plotter
- GLAMM - metabolic networks
- Instructions for installing and running DTASelect - Cravatt Lab
- Cytoscape KGML Reader
- 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)
- How to write a right cover letter when you submit a manuscript:
- Public Speaking:
- 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).
- Lab techniques:
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
WRITING TIPS A useful list of tips for science writing
- National Academies Press [On Being a Scientst: A Guide to Responsible Conduct in Research]
- Nature Authorship Policies []
- A Graduate Student’s Guide to Determining Authorship Credit and Authorship Order: http://www.apa.org/science/leadership/students/authorship-paper.pdf
- PNAS authorship guidelines: http://www.pnas.org/content/101/29/10495.full