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I try to collect hot stuff relevant to biomedical engineering here

Monday, February 25, 2008

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http://www.jhu.edu/nthakor/

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▼ 2008 (39)
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Favorite Quotes

"Try not to become a man of success but rather try to become a man of value" - Albert Einstein
- "Life is like riding a bicycle. To keep your balance you must keep moving" - Albert Einstein
"The only thing that interferes with my learning is my education" - Albert Einstein
"Computer science is no more about computers than astronomy is about telescopes" - Edsger Dijkstra
"Adding manpower to a late software project makes it later" - Brooks's Law
- "Engineering is the art of making what you want from things you can get" - Jerry Avins (?)
"Engineering for me is about being inventive, solving problems, being creative, and actually making things" - James Dyson
"For humans, honesty is a matter of degree. Engineers are always honest in matters of technology and human relationships. That's why it's a good idea to keep engineers away from customers, romantic interests, and other people who can't handle the truth" - Scott Adams
"Hate has a reason for everything. Love is unreasonable" - V. Raiuhes Ahaefvthe
"Tell me and I forget, teach me and I remember, involve me and I learn" -Benjamin Franklin

Signal Detection and Estimation

EE 527: Detection and Estimation Theory (Spring 2008)

Stochastic Calculus

An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations

Optimal Linear Filtering

Kalman Filtering with Newton’s Method
Wiener and Kalman Filtering

Linear Algebra

Symmetric matrices, quadratic forms, matrix norm, and SVD
Making sense of principal component analysis, eigenvectors & eigenvalues
Finding the basis of the intersection of two vector subspaces
Complete (general) solution of undetermined systems
Matrix Analysis and Applied Linear Algebra
Orthonormal Basis and Projection onto a Subspace
Underdetermined Solutions in Maple
Underdetermined Solutions in MATLAB
18.06 Linear Algebra Course at MIT OCW
Toeplitz matrix
Linear Algebra by WWL Chen

Robotics and ROS

RoboticsCourseware.org
How can I use bag file data in Matlab
How to Roslaunch Nodes in Valgrind or GDB

Neuroscience and Neural Engineering

Research of Prof. Josh Tenenbaum
Neural Decoding Code by Dan Morris
Computational Neurscience: Scene Classification Project
Dr. Iyad Obeid's blog
U Washington Neural Engineering
CUNY Introduction to Neural Engineering
MIT's Introduction to Neuroscience
Courses at CNEL lab, Univ of Florida

Information Theory

Maximum Entropy Probabilistic Model
Maximum Entropy: A Blog
A Brief Introduction to: Information Theory, Excess Entropy, and Computational Mechanics
Entropy Matlab library of Rudy Moddemeijer
The Information Structuralist - Blog
Publications on Causality

Probabilistic Graphical Models and Bayes

Nonparametric Bayes by Yee Whye Teh
A reading list on Bayesian methods by Tom Griffiths
Graphical Models and Variational Methods by C. Bishop (videolectures)
Gaussian Mixture Models (Joint, Marginal, Conditional) in Python
GlobalMIT Dynamic Bayesian Networks (DBNs)
Linear Gaussian Models
Gaussian Process Basics (videolectures)
Bayesian or Frequentist, Which Are You? (videolectures)
Dirichlet Processes, Chinese Restaurant Processes, and all that (videolectures)
Conjugate Bayesian analysis of the Gaussian distribution (pdf)
Dirichlet Processes: Tutorial and Practical Course (videolectures)
Should all Machine Learning be Bayesian? Should all Bayesian models be non-parametric? (videolectures)
Nonparametric Bayesian Models in Machine Learning (videolectures)
Graphical Models by Zoubin Ghahramani (videolectures)
Various presentations from John Winn (Microsoft Research)
Introduction to Bayesian Inference by C. Bishop (videolectures)
Sparse Bayesian Models
Bayesian Compressive Sensing
Polya Urn Model
Nonparametric Functional Data Analysis (videolectures)
A Tutorial on Learning With Bayesian Networks

Patents

Patents Top Ten

Music and Engineering

Music, Waves, Physics
Frequency and Music
The Basic Elements of Music
Understanding Basic Music Theory

Real-time One-dim. Signal Drawing

Real-time drawing in C#
Real-time waveform in MATLAB
Nice discussion on GTK

Interesting Personal Websites

Ted Bunn’s Blog
Alex Bikfalvi
Jürgen Pabel's Personal Blog
Dan Morris
John Winn
Robert E. Kass, Prof. of Statistics
Jonathan Brumberg, Ph.D. | Boston University
Rizal's Shade Blog
Daniel James Scott
Marcus Hutter
Chris Evans Development (Computer Vision)
Tyler Streeter
Sargur N. Srihari (Hari)
Rob Hess
João Silva
Pavel Holoborodko
Jack Ganssle
Wookey!
Neil Williams
Brett L. Schuchert
Sven Rosvall
Christopher M. Lott

Open Education and Publication

A semi-comprehensive list of online education resources
12 Dozen Places To Educate Yourself Online For Free
Open Educational Resources Commons
Connexions

FDA -- Medical Devices Software

FDA Validation: a Threat to Free/OSS?
General Principles of Software Validation; Final Guidance for Industry and FDA Staff
Guidance on Off-the-Shelf Software Use in Medical Devices

Design Patterns

User Interface Design Patterns
40+ Helpful Resources On User Interface Design Patterns
Presentation on Factory Pattern
Is-a vs. Has-a
Design Principles and Desing Patterns
Intro to Design Patterns in C++ and Qt 4

Test Driven Development

C/C++ Test Coverage using gcov
Organizing the project tree
C++ Refactoring and TDD with Eclipse CDT and CUTE
Tutorial on TDD using C++
Observations on TDD in C++
CUTE Unit Testing for C++
Mock Objects Paper
Do you believe in Unit Testing for MATLAB?!!
Testing private methods? You bet!

Continuous Integration (SW Development)

C/C++ Test Coverage using gcov
UsingCruiseControlWithCplusPlus
Making the Most of Commit Hooks with Subversion

Version Control

Code Archaeology With Git
An Illustrated Guide to Git on Windows
Git cherry-pick a merge commit
Undo last Git commit
A successful Git branching model
Rebasing Merge Commits in Git
Playing around with git
git: undo all working dir changes including new files
Git tells me my subproject is dirty, what does this mean?
Git - easy way pull latest of all submodules
How to add an empty directory to a git repository
Git: push and delete remote branches
Git ignore
git GUI for Linux
Version Control using git
Version Control with Subversion

Profiling and Memory Debugging

Detecting memory leak with valgrind
Valgrind Memory Debugging and Profiling
Tuning Programs with OProfile
Obtaining Results from OProfile
Smashing performance with OProfile
Looking for Memory Leaks (Mastering J2EE)
Memory Profiling Tools (focused on Java SE)

SW Security

Shell Code Exploits
Buffer Overflow Exploits
Computer Virus Tutorial
Bliss Linux Virus

Coding Standards

C and C++ Style Guides (Archive)
C++ Coding Standard Example
C++ Coding Practices, Style, Standards and document generation (EXCELLENT)
Coding Standard Generator for free!

Software Engineering

Documenting Existing Architectures
UML Component and Deployment Diagrams
UML Tools under Linux
Steve McConnell's Professional Software Development
What do gurus say about Requirements Traceability Matrix?
Traceability Matrix
Traceability on Brad Appleton's ACME Blog
Agile development in a FDA regulated setting
Agile UP: Question Traceability!
Traceability, Agile, and the FDA!
Usage Scenarios Example
Stop writing MRDs and adopt the XP methodology!
Reuse in Use Case Models
Practical UML: A Hands-On Introduction for Developers

ABI

Name Mangling and Call Conventions in C++
How to write shared libraries (all about ELF and shared libraries)
GLIBC_2.4 Not found -- problem and solution
ABI on Wikipedia
What is linux-gate.so.1?

Event-driven Programming

Implicit Invocation
Hollywood Principle
Event Loop
Inversion of Control
Observer Pattern
Event Handler

Qt Software

Programming with C++/Qt on Eclipse
Read this page for nice discussions in the COMMENTS
LGPL 2.1, Qt 4.5 and C++ templates
Keeping the GUI Responsive
Plural Form(s) in Translation(s)
Qt 4 Graphics View
Composition Modes in computer graphics
Fading Effects with Qt 4.1
Transparent Backgrounds in Qt 4.1
The Event Filter and the Observer pattern (from the Qt Quarterly)
Custom Types and QVariant, the MOC (from the Qt Quarterly)
Another Look at Events (from the Qt Quarterly)
C++ GUI Programming with Qt 4 (first edition) legal free download
Intro to Design Patterns in C++ and Qt 4
Writing Unit tests for Qt4 and KDE4 with QtTestLib
Qt/Embedded Official Documentation
Qt/Embedded Virtual Framebuffer
Enabling the Linux Framebuffer
Installing Qt/Embedded
Using Qt to Develop for Embedded Linux

CMake

Testing with CTest
Linking against static libraries
CMake Howto
Building both Debug and Release
link_directories() Command

PC Interfacing Course

Jan Axelson website
Serial Programming Guide for POSIX Operating Systems
Serial Programming HOWTO -- Linux
Parallel Port Output Capabilities
Interfacing the Standard Parallel Port
Interfacing the Enhanced Parallel Port
PRN_IO.c
Interfacing the Serial / RS232 Port

Wikify!

Electronics/How to draw SVG circuits using Xcircuit
Good example for instructions
Linking
Development Stages
Wikibooks:Manual of Style
Featured Wikibooks Criteria
A Complete Book on Wiki Markup
TeX Markup
Advanced Techniques
Wikibooks:Sandbox
Wiki-Markup
How To Edit A Wikibook
Discussion and Consensus
Wikipedia:How to create graphs for Wikipedia articles

Academia

Advice for Prospective Research Students
38 tips on writing an academic CV
How to Be a Good Graduate Student
A Guide to Writing a Successful Paper
Writing Homework Assignments
Manual for Writing Mentors
Write 2 Teach in 3 Days
Research methods
World Academy of Science, Engineering and Technology
What is a thesis defense?

Marketing, Strategic Management, and Others...

How to Write an MRD
MRDs, PRDs, FRSes, and SRSes
Requirements Document Alphabet
Open Source Startup Marketing: Initial Steps
SWOT analysis method and examples, with free SWOT template
SWOT Analysis

ECG

Open Medical (resources for ECG signals and files)
Advanced Methods for ECG Analysis Source Code
Cardiovascular Physiology Concepts
Cardiology Explained Book (Stanford Uni)
Standard Normal ECG
A practical guide to ECG monitoring and recording
LabVIEW for ECG Signal Processing
Computers in Cardiology
Bioelectromagnetism -- Online Book (Ch15)

TeX and LaTeX

Handling IEEE PDF Express in LaTeX
Typesetting your academic CV in LaTeX
LaTeX Resources
LaTeX Style and BiBTeX Bibliography Formats for Biologists
LaTeX Tutorial by Prof. Slim Abdennadher (GUC)
Online help for LaTeX
Beamer Simple Examples
A Beamer Tutorial in Beamer
LaTeX for Master Thesis
LaTeX Resume Tips
Daniel Lamblin's Resume
LaTeX CV Template
Making plots using Octave, gnuplot, and LATEX
Graphs in LaTeX using GNU Octave
More LaTeX on Athena: MIT Thesis (AC-52)
MS-Word is Not a document exchange format
LaTeX and Microsoft Word
LaTeX Hacks - Nice Collection
Document Revisions for LaTeX
Cusom Headers and Footers
LaTeX Resume Class
BeamerPoster (Excellent)
SPIE LaTeX Style Files
LaTeX: from quick and dirty to style and finesse
LaTeX@dd: many practical hints
pdfLaTeX presentation How-To
A short example of how to use LaTeX for scientific reports
Color Package Demo
LaTeX Wikibook

Control Systems

PID Tuning by Abdul Aziz Ishak
Controllability of dynamical systems (a review)
Controllability and Observability
ECE 602 Lumped System Theory

Colors!

Are Red, Yellow, and Blue primary colors?

Machine Learning

Scikit-learn: Machine Learning in Python
TunedIT Rseslib: Machine Learning Library in Java
TunedIT Data Mining Blog
What skills are needed for machine learning jobs?
Kernel Machines Library in C++
Dlib - Machine Learning Library in C++
Machine Learning Course at Carnegie Mellon University
Machine Learning Video Playlist
Teaching Materials
Simplified Introduction -- Machine Learning: A Love Story
Introduction to Support Vector Machines (videolectures.net)
Machine Learning Course at Stanford Engineering
Precision and Recall
BOOK: Pattern Recognition and Machine Learning. Christopher M. Bishop
Neural Networks Basics

Probability and Statistics

Non-homogenous Poisson Process (w/ MATLAB)
Secrets of Good Correlations
Comparing groups for statistical differences: how to choose the right statistical test?
Characteristic Functions for Discrete RV's
StatSoft Statistics Textbook
Statistical Notes
Applets for "Random Signals and Noise"
Ant Sort: Bringing Order out of Chaos
Linux Magazine - Live Random or DieHarder
RANDU (Wikipedia)
Pseudorandom number generator (Wikipedia)
Linear congruential generator (Wikipedia)
JHSPH OpenCourseWare >> 2004-05 Biostatistics Lecture Series
Collaborative Statistics Textbook

Computer Vision

Computer Vision Resources (up-to-date)
Book-- Computer Vision: Algorithms and Applications
RANSAC for Dummies!
The Computer Vision Homepage at Carnegie Mellon University
Stanford Vision Lab (Dr. Li Fei-Fei)
A book by Dr. Simon Prince
Computer Vison Concepts from a Machine Learning Perspective (Video Lectures)
Computer Vision Central
Computer Vision (and OpenSURF) by Chris Evans
USC Computer Vision Group (Papers)
Selected Topics in Computer Vision - EPFL
Computer Vision - Lecturer: Prof. Pascal Fua - EPFL
Computational Perception Wiki
Camera Calibration Toolbox for MATLAB
MATLAB and Octave Functions for Computer Vision and Image Processing
MATLAB Functions for Multiple View Geometry
BOOK: Multiple View Geometry in Computer Vision
University of Nevada (CV Course)
Geometirc Operations

Symbolic / Numerical Analysis

The YACAS Computer Algebra System
Arbitrary-precision numerical programming

Digital Image Processing

The Hypermedia Image Processing Reference
Image resizing and enhanced digital video compression
DIGITAL IMAGE INTERPOLATION

DSP - Advanced

Linear Prediction and Prony's Method
FIR filter to IIR using MATLAB
Spectrum and spectral density estimation by the DFT
KissFFT for Real Signals
KissFFT Scaling
Multirate DSP, part 1: Upsampling and downsampling
Filter banks, part 1: Principles and design techniques
Image Anti-aliasing at GPU Gems
Multirate DSP, part 3: ADC oversampling
A WAVELET TOUR OF SIGNAL PROCESSING

DSP - General

DSP Tricks: Doing Zero-phase filtering
INTRODUCTION TO DIGITAL FILTERS WITH AUDIO APPLICATIONS JULIUS O. SMITH III
Smooth noise-robust differentiators
Savitzky-Golay Digital Differentiators
Central Difference Approximations
e-dsp.com (Excellent)
Rick Lyons Blog on DSPRelated.com
Steve Smith Blog on DSPRelated.com
Digital Signal Processing/Using MATLAB (Wikibooks)
Signals and Systems (Wikibooks)
ADCs for DSPs, part 1
DSP Tricks: Interpolating a bandpass signal
DSP Tricks: Spectral leak location algorithm
Digital Signal Processing Tricks - Frequency Translation without multiplication
Java Applets for DSP Concepts
DSPRelated
dspGuru

Embedded Linux Graphics

GUI Document, a good start point
Multimedia in embedded Linux systems
More Qt Licensing
Qt Licensing
GTK+ Embedded using DirectFB
Linux Devices Excellent Article

Embedded Linux - Realtime

RapidReboot using kexec -- Ubuntu Wiki
Reboot Linux faster using kexec
Booting Linux: The history and the future
RTOS versus GPOS: What is best for embedded development?
Guide to POSIX Real-time Programming
"Real time" signals on Linux
Anatomy of real-time Linux architectures
Real-time Square Wave Example
RT_PREEMPT_HOWTO
Ingo Molnár -- The RT patch maintainer

Embedded Linux

PTXdist - Reproducable Embedded Linux Systems
strace: The Friend You Never Knew You Had
Embedded Linux Platforms
GNU/Linux from eight miles high
(EXCELLENT) Linux Development Toturial -- How to Participate in the Linux Community
Kernel Boot Messages
MontaVista Contributes to Open Source for CE Linux
TinyGentoo (very good)
Is Linux Free? (Article)
(EXCELLENT) Free Software tools for embedded systems
Embedded Linux Quick Reference Guide (Part 4)
Embedded Processor and System-on-Chip Quick Reference Guide
(Excellent) Do-it-yourself embedded Linux development tools

FPGA

VHDL Tutorial (EXCELLENT)
FPGA from scratch (EXCELLENT)
Veripool -- Free Verilog and SystemC Software
Verilog.NET
Aldec Downloads - Tutorials and Software
Xilinx on Linux HOWTO
The Designer’s Guide to Verilog -- Online
Verilog more books
Verilog and VHDL books
VHDL Cookbook e-books
FPGA Libre
FPGA-based hardware acceleration of C/C++ based applications - Part 3
Translate the high-level DSP algorithm to RTL in an FPGA
How to design an FPGA from scratch
FPGA-based hardware acceleration of C/C++ based applications - Part 3

SPICE

SPICE Algorithm
SPICE Basics

MATLAB / Octave

Working with Arrays of Structures
Numerical Computing with MATLAB by Cleve Moler
MATLAB Primer, Stanford
MyOctave Blog (helpful)
Getting Started Video Tutorial
Signal Processing using MATLAB (labs)
MATLAB Educational Websites
Student Tutorials on the Mathworks website
MATLAB tutorial at the University of Florida
MATLAB tutorial on the MIT
Signal Processing Examples on MATLAB
What are your favourite Matlab/Octave programming tricks?
Matlab Programming for DSP
MATLAB-to-C translation, part 1: Pitfalls and problems
GNU Octave: Debugging
GNU Octave - Functions and Scripts
Octave Programming Tutorial (Wikibooks)
MATLAB Programming/Differences between Octave and MATLAB
MATLAB Programming (Wikibooks)
MATLAB speed optimization

Open Source - General

Why the Public Domain Isn't a License
Architecting Peaceful Coexistence: Open Source/Proprietary Code
LGPL 2.1, Qt 4.5 and C++ templates
Open Content
A Practical Guide to GPL Compliance
FOSSology - Analyzing your code for FOSS
Open Source Alternative to Commercial Software
Please avoid sending me Word or PowerPoint attachments

Ubuntu

Light-weight Ubuntu :)
Unofficial Ubuntu Gutsy Starter Guide
Ubuntu Tips and Tricks (Excellent)
Ubuntu and Debian
DesktopTeam/Specs/HardyHardwareDetection
Reporting Bugs
Malicious Commands
How To Test Hardy, File Bugs and Repair Breakage
Bulk renaming of files using a Perl script
Bug Reporting -- Find the right package (VIP)
Ubuntu Mirrors

OpenSuSE

Package_Repositories
Additional YaST Package Repositories
Mirrors (Released Version)
Add_Package_Repositories_to_YaST

Networking

How_to_setup_a_public_server_using_the_D-Link_DSL-502T_ADSL_Router
Course Materials for Networks
Linux Tutorial Networking
Ping: ICMP vs. ARP

Linux/UNIX

10 things C C++ Linux Programmer must know
UNIX Shell Scripting Tutorial
Linux Shell Scripting Tutorial
Bash by example
How to Daemonize a Process (BitTorrent)
ext4 File System: Introduction and Benchmarks
Libraries on Linux
Stay curious!What does “> /dev/null 2>&1″ mean?
Top 10 Software Development Articles of 2008
Top 10 Sys Admin Articles of 2008
Manipulating and organizing files
Great Linux articles at Linux.com
Download Linux! Most popular Linux distributions
ACPI HOWTO Shutdown headless server when power-button pressed
No games for Linux?
Steve Parker Shell Scripting Tutorial
LPI Linux Certification (Wikibook)
Linux IO Redirections (Important)
Real-life find usage
Sed - An introduction and tutorial
Using the versatile (find) utility
Bourne_Shell_Scripting
Learning_the_vi_editor
UNIX_Computing_Security
Linux Command Line For Newbies :)
A Good Free UNIX book
FUN: What your choice of Linux distribution says about you
diff3
Linux Kernel Development (2nd Edition)
Your UNIX: The Ultimate Guide
GNU/Linux Application Programming
Rute User's Tutorial and Exposition

Debian

Remote Desktop using XRDP
An OUTDATED but excellent tutorial
How to use apt-get behind proxy server
SATA Shutdown Bug
Debianist (Troubleshooting by a Debian Guru)
Maintaining a mixed debian system

Doxygen and JavaDoc

How to Write Doc Comments for the Javadoc Tool
Documenting the code (Doxygen Manual)

Obfuscated Code

Just Another Perl / Unix Hacker
Xmas program to test GCC
A tricky c program
A few small obfuscated Programs

GCC

Solving circular dependency during linking
Compiling a compiler
Software optimization resources
gcc Optimization Tutorial

Programming - Multithreading

EXCELLENT POSIX Threads Tutorial
POSIX Threads Tutorial
OpenMP article

Programming - C++

Ten C++11 Features Every C++ Developer Should Use
High Resolution Time Measurement in C/C++
Time Measurement in C/C++
const keyword in C++ versus Java (Wikipedia)
Dive in to C++ and survive (embedded C++)
Programming -- Principles and Practice Using C++ (by the C++ inventor!)
C and C++ Style Guides
Intro to Design Patterns in C++ and Qt 4
C++ Lookup Rules (EXCELLENT)
Strings in C++
Coding Standard Generator for free!
Compatibility of C and C++ (Wikipedia)
C++ Coding Practices, Style, Standards and document generation (EXCELLENT)
Using and Extending Namespaces
C++ Coding Standard Example

Programming - C

Bit Twiddling Hacks
Heap overflow!!
Tasks (the program running)
User Memory Management (Stack, BSS, Data, ...)
Understanding Memory (Stack, BSS, Data, ...)
Expert Stuff about C
Doing C code unit testing on a shoestring: Part 1
C Program Examples

Embedded Systems

Good articles from netrino.com
Why C++ is a viable alternative to C in embedded systems design
Power consumption optimization by writing efficient code!
Debugging embedded C
Embedded System Design: A Unified Hardware/Software Introduction
Thermal Budget in Embeded Systems
How to write secure C/C++ application code for your embedded design: Part 1
There is no such a thing as an embedded system !
The basics of embedded programming: Part 9
Embedded Books Reading Room - October, 2007 (Updated!)
Products TearDown
Embedded Systems
Building Bare-Metal ARM Systems with GNU: Part 10
PRODUCT HOW-TO: Locating and measuring sources of EFD and ESD burst interference
Trace exposes the toughest real-time bugs (PERL)
The basics of programming embedded processors
Kunal Singh Website

Fourier Stuff

Fourier Synthesis
Fourier Series: Eigenfunction Approach

Search Engines

ScientificCommons.org
Use google to search WASET
EUL Egyptian Databases
The Engineering Search Engine
SCIRUS - Scientific Search Engine

Engineering Links

Engineering Fundamentals
The Engineering Search Engine

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BioEng Student: Biomedical Engineer

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