Protocols

Frequently used laboratory protocols are found on Google Drive. Only laboratory members can access the drive.

Resources

The laboratory also organizes a number of research support networks at the University of Texas at Dallas. Please contact Dr. Tae Hoon Kim for more information.

ONLINE RESOURCES

Safety

• Yale EHS Waste Forms

• Yale Biological Safety

• Biosafety Manual

• Clean Air Device Manual

• Spill Guide

• Chemical Hygiene

• Hazardous Waste

• Biomedical Waste Procedure

• Glove Permeation Chart

• Shipping Form

Online Protocol Repositories

• BioTechniques Protocol Guide

• Cold Spring Harbor Protocols

• Nature Protocols

• Protocol Online

• Springer Protocols

• Wiley’s Current Protocols

Genome Engineering

• CRISPR genome editing tools

Next Generation Sequencing

• Sequencing Library Protocols

• Information on bulldog HPC cluster

General Software

• Yale Academic Media & Technology

• Unix and Perl Primer for Biologists

• Python tutorial

• Scientific Tools for Python

• SQL tutorial

• Sequel-Pro - SQL database management for MacOS X

Research related applications

• Wolfram Alpha

• Database of Useful Biological Numbers

• serial cloner manipulates DNA sequences - similar to Ape but with more features

• this site contains following programs:

  • 4peaks - view sequence chromatograms

  • enzymeX - restriction digest analysis

  • iRNAi - select siRNA sequence

  • lab assistant - timer, lab journal keeper, to do lists

  • papers - organize PDFs

• skim - another program to organize PDFs

• Broad Institute Software

• Handbook of Biological Statistics

• ENCODE Project Statistics

Sequence Analysis

• Bioinformatics Links Directory

• Sequence Manipulation Suite

• double digest chart

• double digest calculator

• enzyme lookup

• buffer chart

• DNA logos

• primer3

• box shader

• galaxy

• taverna

• The Genome Analysis Toolkit

• SAM Tools

• Gerald server for Illumina data retrieval

• MAQ

• bowtie

• cufflinks

• tophat

• cummeRbund

• Integrative Genome Browser (IGV)

• Circos Software for circular visualization of the genome

• Microarray Software Suite

• Partek Genomic Suite

• sicer

• eXpress a generic platform for quantifying sequence abundance from next gen sequencing data

• Homer Software for analysis of ChIP-seq and HiC data

Array Analysis

• Java Treeview

• Cluster 3.0

• Mpeak

Research Databases

• UCSC genome browser

  • In-Silico PCR

• EnsEmbl

  • KaryoView

• Entrez

  • PubMed

  • BLAST

• GNF SymAtlas

• Cancer Expression Module

• Connectivity Map

• NCBI dcode

• bioinformatics directory

• Human Gene Mutation Database

• polycomb database

• Knockout Mouse Database

Motif Analysis

• CisEvolver

• COTRASIF

• CREAD

• JASPAR

• cisRED

• CEAS

• OREGANNO

• MEME

• NestedMICA

• TRANSFAC motif search

• distant regulatory elements

• Gene Regulation Tools at Zlab

• Webmotifs

• Tmod

• STAMP motif comparison tool

Network Analysis

• Cytoscape Network Visualization Software

Modeling

• model-based global analysis of experimental data

• Systems Biology

Programming References

• R project R wiki

• Bioconductor

• MySQL

• Perl

  • Picking up Perl

  • PerlMonk's Tutorial

  • Bioinformatics: Writing Software for Genome Research

  • The perl.org Online Library

• MatLab Tutorial

• Google University Consortium

• Open Helix Tutorials

Scientific Blogs

• Biomedexperts.com

• InnoCentive

• Nature Networks

• ScholarOne

• Scientist Solutions

• The Science Advisory Board

FUNDING AND CAREER DEVELOPMENT

Main Funding Bodies

• grants.gov

• proposalcentral

• NIH Office of Extramural Research

• SF424 Forms

• Non-Competing Continuation Progress Report PHS 2590

• How to fund science

• Health Resources in Action

Predoctoral Fellowships

• Army Medical Research Programs (CDMRP)

• National Science Foundation's Graduate Research Fellowship Program

• PhRMA Foundation

Postdoctoral Fellowships

• AAAS

• American Association for Cancer Research

• American Cancer Society

• Army Medical Research Programs (CDMRP)

• Burroughs Wellcome Fund

• Cancer Research Institute

• Damon Runyon Cancer Research Fund

• EMBO

• FRAXA Research Foundation- Fragile X

• Helen Hay Whitney Foundation

• Hereditary Disease Foundation Lieberman Award

• HFSP

• Hunter's Hope.org

• Leukemia & Lymphoma Society

• Leukemia Research Foundation

• Life Sciences Research Foundation

• L'Oreal USA Fellowships For Women in Science

• March of Dimes

• MMRF Research Grants

• Multiple Sclerosis Society

• Muscular Dystrophy Assocaition

• National Hemophilia Foundation Research

• New York Stem Cell Foundation

• PhRMA Foundation

• Prevent Cancer Foundation

• Prostate Cancer Foundation

Transition and Foundation Grants

• AACR

• Alliance for Cancer Gene Therapy

• Beckman Foundation

• Burroughs Wellcome Fund

• Department of Defense

• John Templeton Foundation

• Leukemia & Lymphoma Society

• Leukemia Research Foundation

• M. J. Murdock Charitable Trust

• March of Dimes

• McDonnell Foundation

• New York Stem Cell Foundation

• Packard Foundation

• Pardee Foundation

• Pew Scholars

• PhRMA Foundation

• Prostate Cancer Foundation

• Research Corporation for Science Advancement

• St. Baldrick's Foundation

• Searle Scholars Program

• Sidney Kimmel Cancer Research Foundation

• Whitaker International Fellows and Scholars Program

• NIAID list of foundations

Career in Science

• Making the Right Moves

• Future of PhDs