Research Tools


Here is a selection of some online tools that I have found helpful in my research. 


General Research Tool Links

Jane - Journal/Author Name Estimator
    An interesting text-heuristic article search engine, which makes a good complement to PubMed.

BioNumbers
    A catalog of numbers about biology, such as the number of mRNA transcripts per cell, or the diffusion constant of a given protein.  Especially useful for quantitative biology, but still a work in progress.

iGEM - International Genetically Engineering Machine competition
    International competition where teams of undergraduates work on a synthetic biology project, and present their results at a conference at MIT.  I was on the 2007 Berkeley iGEM Team, and would certainly recommend it to any undergraduates either interested in synthetic biology, or wanting a good introduction to wet-lab research.

Genomics Research Tool Links

Genome Analysis Tool Kit (GATK)
    A comprehensive toolkit to analyze next-generation sequencing data for genomic studies.  I used this toolkit in my network enrichment project in the Wall Lab.

GeneMANIA
    Gene function predictor and network database, including many genetic interaction networks I have used.

Plink
    Tool for quality control and analysis of next-generation sequencing data.
 

Zebrafish Research Tool Links

ZFIN
    General database for Zebrafish information including: genes, alleles, journal articles, mutants, and much more.

Ensembl Zebrafish Genome
    Genomics tool, great for searching for sequences, looking up genes, etc. This link is to the Zebrafish page, but Ensembl has many other genomes as well.
 

Harvard Library Proxy Bookmarklet

This tool that I made allows users of the Harvard Library Proxy to redirect the page they are on to the proxy served page, in one click.

Supported browsers include: Firefox, Google Chrome, Safari, Internet Explorer

To install this bookmarklet, right click (or control-click for mac) on the link and select "Bookmark This Link" or "Add to favorites...":

Harvard Library Proxy Bookmarklet

(If it is visible, you can also drag this link into your bookmarks toolbar/favorites bar)

 









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