Jul 29, 2015

I am writing new lectures and organizing a lot of teaching material to teach 4 (!) classes this fall at two different universities (NYU and Fordham). I would like to keep the teaching materials in a nice easily accessible online location, and easily share with my students without a lot of hassle to sign them all up or whatever. I had a fairly good experience with Google Drive for a short course this Spring, so I'm trying it out now. Here is the master link to all of my 2015 teaching material:


Stuff will appear, change, possibly disappear from this location as I keep sorting and rewriting, up to and during the classes. Most of the material is my own, some journal articles that I provide as readings to my students, and some shameless theft of good lectures, exercises, and tutorials from other folks smarter or better at explaining stuff than I am.

We are also planning to make Screencast type videos of most of the lectures, which get dumped on YouTube. I will try to find some sensible way of organizing them and sharing via this NGS blog.

Jul 16, 2015

CSHL Press has made the RNA-seq chapter of my Next-Gen Seq book available free from their website: RNA Sequencing with Next-Generation Sequencing.


Cold Spring Harbor Laboratory Press banner image
Next-Generation DNA Sequencing Informatics, Second Edition banner image

May 28, 2015

New 'Next-Gen Seq 2' book is at the printer

The second edition of the Next-Generation Sequencing Informatics book (that I edit) is at the printer and available for pre-order at Cold Spring Harbor Press and Amazon. We think it will ship on June 30th, maybe a bit sooner.

[James Hadfield at CoreGenomics blog has posted a review: http://core-genomics.blogspot.co.uk/2015/05/book-review-next-generation-dna.html ]

We have added new chapters on the latest sequencing technology, QC, de novo transcript assembly, proteogenomics and lots of updates and expansion in areas such as RNA-seq and ChIP-seq. It has a beautiful cover and its not too expensive.

Here is the official publication blurb:

Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making genome and RNA sequencing an affordable and frequently used tool for a wide variety of research applications including variant (mutation) discovery, gene expression, transcription factor analysis, metagenomics, and epigenetics. Bioinformatics methods to support DNA sequencing have become and remain a critical bottleneck for many researchers and organizations wishing to make use of NGS technology. Next-Generation DNA Sequencing Bioinformatics, Second edition, provides thorough, plain language introduction to the necessary informatics methods and tools for analyzing NGS data as did the first edition, and provides detailed descriptions of algorithms, strengths and weaknesses of specific tools, pitfalls and alternative methods. Four new chapters in this edition cover: experimental design, sample preparation, and quality assessment of NGS data; Public databases for DNA Sequencing data; De novo transcript assembly; proteogenomics; and emerging sequencing technologies. The remaining chapters from the first edition have been updated with the latest information. This book also provides extensive reference to best-practice bioinformatics methods for NGS applications and tutorials for common workflows. The second edition of Next-Generation DNA Sequencing Bioinformatics addresses the informatics needs of students, laboratory scientists, and computing specialists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies.

and the Table of Contents:

1) Introduction to DNA Sequencing
Stuart M. Brown
2) Quality Control and Data Processing
Stuart M. Brown
3) History of Sequencing Informatics
Stuart M. Brown
4) Public Sequence Databases
Stuart M. Brown
5) Visualization of Next-Generation Sequencing Data
Philip Ross Smith, Kranti Konganti, and Stuart M. Brown
6) DNA Sequence Alignment
Efstratios Efstathiadis
7) Genome Assembly Using Generalized de Bruijn Digraphs
D. Frank Hsu
8) De Novo Assembly of Bacterial Genomes from Short Sequence Reads
Silvia Argimón and Stuart M. Brown
9) De Novo Transcriptome Assembly
Lisa Cohen, Steven Shen, and Efstratios Efstathiadis
10) Genome Annotation
Steven Shen and Stuart M. Brown
11) Using NGS to Detect Genome Sequence Variants
Jinhua Wang
12) ChIP-seq
Stuart M. Brown, Zuojian Tang, Christina Schweikert, and D. Frank Hsu
13) RNA-seq with Next-Generation Sequencing
Stuart M. Brown and Jeremy Goecks
14) Metagenomics
Guillermo I. Perez-Perez, Miroslav Blumenberg, and Alexander V. Alekseyenko
15) Proteogenomics
Kelly V. Ruggles and David Fenyö
16) DNA Sequencing Technologies and Applications
Gerald A. Higgins and Brian D. Athey
17) Cloud-based Next-Generation Sequencing Informatics
Konstantinos Krampis, Efstratios Efstathiadis, and Stuart M. Brown

Feb 9, 2015

Password hell

This is not a Bioinformatics post, just an amusing technology catch-22 that I encountered this morning. At NYU we have automatic mandatory password updates for our accounts with IT. This includes email, login to my Windows desktop computer, and wireless devices on the secure WiFi network in our building. Since I am lazy about these things, I did not heed the warnings and follow the instructions in the "Password Update" email from our IT Department. Instead, at home on Sunday night, I got a message when I tried to log in to my email account saying that I should update my password, and a helpful little box appears where it is possible to type old password and new password, hit submit and its all good.

I made a new password, and checked my mail, but after about 5 min, I got knocked off the network and can't log back in. It's late, so I figure to deal with it at the office in the morning. At my desk, I can't log into my computer (uses the same network "kerberos" password), and my phone complains that it can't get on the local wireless network. I try new password, old password, and eventually get the helpful message that my account has been locked by the IT Dept, and I must call the helpdesk. Its 9 AM on Monday and the helpdesk picks up right away. Help Guy asks if I have any wireless devices that may be using the old password. I look at the offending iPhone, and shut off WiFi. Helpdesk says: "I still see wireless activity hitting your account with an invalid password." Back to my desk, where my desktop Mac is using WiFi and getting unhappy messages from the network. Shut down WiFi. Helpdesk still sees activity on my account. Think, think?? Into the drawer where I have a laptop that we use for teaching and public seminars, it is asleep, but somehow still hitting the wireless network with my old password. Turn off WiFi on that one, and finally the helpful helpdesk guy can unlock my account. Then I can go back to each device and rejoin the network with the new password. I guess I'm not the first idiot this has happened to. Moral of the story??? Follow instructions very carefully or your helpful technology tools will gang up against you.

Happy Ice Storm Day from New York

Sep 10, 2014

Introduction to Biostatistics and Bioinformatics course at NYUMC

We are giving a new course in the PhD program at NYU Med School (Sackler Institute) this semester called "Introduction to Biostatistics and Bioinformatics". It will have a mixture of lectures on Bioinformatics, Biostatistics, and Python programming. Hopefully we will be able to show the students the intersection of these topics as something like "Data Science for Biology".  Lecturers will be myself, David Fenyo, Judy Zhong, and Pamela Wu.

Course Overview
The goal for the Introduction to Biostatistics and Bioinformatics course is to provide an introduction to statistics and informatics methods for the analysis of data generated in biomedical research. Practical examples covering both small-scale lab experiments and high-throughput assays will be explored. The course covers a wide range of topics in a short time so the focus will be on the basic concepts, and in the practical programming exercises the students explore these basic concept and common pitfalls. An introduction of basic Python and R programming will be given throughout the course and many exercises will involve programming.

The lectures will be posted to YouTube each week. Here are our first ones from yesterday:
Intro Lecture/Data Visualization:  http://youtu.be/YDUPzq7i49U
Python programming #1:  http://youtu.be/r2N-thn7j4o

The course curriculum and links to lecture slides (PPT), readings, and various handouts and exercises is here:   http://fenyolab.org/ibb2014