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Information and Publications: Showing

ACEDB Genome Database Software FAQ

ftp://rtfm.mit.edu/pub/faqs/acedb-faq (At MIT)

Books: Showing

Biometrics: Identity Verification in a Networked World
[Samir Nanavati, et al; 2002-03-15] ISBN 0471099457
- At Barnes & Noble - At Amazon - At Half

Conservation Biology and Landscape Ecology : Spreadsheet Exercises
[Therese M. Donovan, Charles W. Welden; 2001-12] ISBN 0878931597
- At Barnes & Noble - At Amazon - At Half

Beginning Perl for Bioinformatics
[James D. Tisdall; 2001-10-15] ISBN 0596000804
- At Barnes & Noble - At Amazon - At Half

Developing Bioinformatics Computer Skills
[Cynthia Gibas, Per Jambeck; 2001-04-15] ISBN 1565926641
- At Barnes & Noble - At Amazon - At Half

Computational Modeling of Genetic and Biochemical Networks
[James M. Bower (Editor), Hamid Bolouri (Editor); 2001-01-22] ISBN 0262024810
- At Barnes & Noble - At Amazon - At Half

Perl for Bioinformatics
[Arun Jagota; 2001-01-15] ISBN 0970029721
- At Barnes & Noble - At Amazon - At Half

Computational Molecular Biology: An Introduction
[Peter Clote, Rolf Backofen; 2000-09-22] ISBN 0471872520
- At Barnes & Noble - At Amazon - At Half

Computational Molecular Biology
[Pavel A. Pevzner; 2000-08-21] ISBN 0262161974
- At Barnes & Noble - At Amazon - At Half

Dorland's Electronic Medical Dictionary
[; 2000-08] ISBN 0721694934
- At Barnes & Noble - At Amazon - At Half

Introduction to Computational Molecular Biology
[Joao Carlos Setubal (Contributor), et al; 1997-01-16] ISBN 0534952623
- At Barnes & Noble - At Amazon - At Half

Evaluation Methods in Medical Informatics
[Charles P. Friedman, Jeremy C. Wyatt (Editor); 1997-01-15] ISBN 0387942289
- At Barnes & Noble - At Amazon - At Half

Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology
[Dan Gusfield; 1997-01-15] ISBN 0521585198
- At Barnes & Noble - At Amazon - At Half

Articles: Showing

An Emerging Biometric API Industry Standard ( Catherine J. Tilton ; IEEE Computer Magazine 2000-02)

BioID: A Multimodal Biometric Identification System ( Robert W. Frischholz, Ulrich Dieckmann ; IEEE Computer Magazine 2000-02)

- By combining face, voice, and lip movement recognition, this identification system yields highly accurate results. Because it includes a dynamic feature, it provides more security than systems using only static features.

An Introduction to Evaluating Biometric Systems ( P. Jonathon Phillips, Alvin Martin, C.l. Wilson, Mark Przybocki ; IEEE Computer Magazine 2000-02)

- How and where biometric systems are deployed will depend on their performance. Knowing what to ask and how to decipher the answers can help you evaluate the performance of these emerging technologies.

An Iris Biometric System for Public and Personal Use ( Michael Negin, Thomas A. Chmielewski, Marcos Salganicoff, Theodore A. Camus, Ulf M. Cahn von Seelen, Péter L. Venetianer, Guanghua G. Zhang ; IEEE Computer Magazine 2000-02)

- The human iris promises to deliver a level of uniqueness to identification applications that other biometrics cannot match. The authors describe a working system used in the UK and in pilot projects worldwide.

Guest Editors' Introduction: Biometrics-The Future of Identification ( Sharath Pankanti, Ruud M. Bolle, Anil Jain ; IEEE Computer Magazine 2000-02)

- It is too early to predict where, how, and in which form reliable biometric services will eventually be delivered. But it is certain that there is no way around biometrics-based identification if we insist on positive, reliable, and irrefutable identification.

Federal Biometric Technology Legislation ( James L. Wayman ; IEEE Computer Magazine 2000-02)

- The government's interest in biometric technologies is motivated by the desire to improve the delivery of services to citizens by increasing efficiency and convenience while decreasing costs and fraud. However, the very personal nature of this technology raises concerns about its potential impact on personal freedoms.

Biometrics: A New Era in Security ( George Lawton ; IEEE Computer Magazine 1998-08)

Surgical Planning for Liver Resection ( Elliot K. Fishman, Brian S. Kuszyk, David G. Heath, Luomin Gao, Brian Cabral ; IEEE Computer Magazine 1996-01)

- Effective surgical planning requires 3D images that show tumor location relative to key blood vessels. This research uses volume rendering of CT data to meet these requirements.

An Optical Navigator for Brain Surgery ( Ludwig Adams, Achim Knepper, Dietrich Meyer-Ebrecht, Rainer Rüger, Willem van der Brug ; IEEE Computer Magazine 1996-01)

- An orientation device to aid physician accuracy in brain surgery has been developed by combining 3D position measurement techniques, digital image processing, and 3D display techniques.

Computer-Aided Surgery Planning and Rehearsal at Mayo Clinic ( Richard A. Robb, Dennis P. Hanson, Jon J. Camp ; IEEE Computer Magazine 1996-01)

- Doctors use interactive technology and computer-generated 3D images of patients' bodies to plan and rehearse surgery, so it will be more effective, less risky, and less expensive.

Two-Handed Spatial Interface Tools for Neurosurgical Planning ( John C. Goble, Ken Hinckley, Randy Pausch, John W. Snell, Neal F. Kassell ; IEEE Computer Magazine 1995-07)

- A computer-based neurosurgical planning system lets neurosurgeons easilymanipulate 3D data using their everyday skills from handling tools with twohands. It has been tested in actual surgical procedures.

Computer Simulations of Protein Dynamics and Thermodynamics ( David Case ; IEEE Computer Magazine 1993-010)

- The computational challenges of producing realistic biomedical simulations are reviewed. Techniques for applying classical mechanics simulation methods to proteins and ways to solve Newton's equations are discussed. Two recent applications of these methods are examined. The first considers the rate at which molecular oxygen binds to myoglobin, an oxygen-storage protein found in muscle. The second application involves the thermodynamics of the binding of oxygen to hemoglobin, a protein that is the major component of red blood cells. The comparison of this biochemical event to one in which oxygen is bound to an unusual variant of hemoglobin illustrates many of the simulation methods commonly used in the pharmaceutical industry to aid in the drug discovery process.

Computational Medicine: Bioelectric Field Problems ( Christopher R. Johnson, Robert S. MacLeod, Michael A. Matheson ; IEEE Computer Magazine 1993-010)

- Applications of large-scale computer modeling and simulation to a class of bioelectric field problems in a variety of biomedical research areas, from single cells to full human structures, are described. The authors focus on a specific subset of bioelectric field problems that have applications in electrocardiography and electroencephalography. The physics and physiology of bioelectric volume conductors are introduced. A specific computational example and the authors' view on the future direction of computational medicine are presented.

Models for Molecular Computation: Conformational Automata in the Cytoskeleton ( Stuart R. Hemeroff, Judith E. Dayhoff, Rafael Lahoz-Beltra, Alexei V. Samsonovich, Steen Rasmussen ; IEEE Computer Magazine 1992-11)

- The structure and conformational dynamic changes that occur in cytoskeletal proteins within living cells and evidence for their participation in computational processing are described. The role of cellular automata, in which lattice subunits with discrete states interact only with nearest neighbors, in molecular computing is discussed. Simple rules governing subunit neighbor interactions can lead to complex behaviour capable of computation. It is shown that cellular automata may be implemented in the conformational relationships among neighboring protein subunits of cytoskeletal polymers including microtubules, and microtubule conformational automata networks may signal, adapt, recognize, and subserve neural-level learning.

An Approach to Computational Complexity: Nondiscrete Biomolecular Computing ( Nikolay G. Rambidi ; IEEE Computer Magazine 1992-11)

- Discrete molecular computing devices based on digital device simulation and nondiscrete biomolecular computing devices based on the overall principles of information processing that use molecular-level mechanisms to create simple biomolecular systems are described. It is argued that discrete molecular computing only extends the choice of materials available in modern semiconductor device technology, but does not provide an opportunity to use physical mechanisms of information processing different from those available in conventional materials and devices. Nondiscrete biomolecular information processing devices effectively solve some problems with high computational complexity-for example, image processing operations such as contour enhancement and line extraction. The information processing potential of biomolecular systems is reviewed.

Interconnection-Free Biomolecular Computing ( Takafumi Aoki, Michitaka Kameyama, Tatsuo Higuchi ; IEEE Computer Magazine 1992-11)

- The basic concept of interconnection-free biomolecular computing and its realization in a computing model based on the massive, natural parallelism between enzymes and their substrates are described. An approach to implementing the model is presented. The approach involves two primitive switching functions: detecting specific substrates in solution using enzyme-based biosensors and producing specific substrates in response to the electric signal from the biodevice's selection function. The major challenges involved in implementing the computational model are reviewed.

Biologic Computational Building Blocks ( Myles H. Capstick, W.P. Liam Marnane, Ronald Pethig ; IEEE Computer Magazine 1992-11)

- Methods to represent the biological activity of oxidoreductase enzymes using logic state diagrams and to simulate the enzymes' functionings using synchronous sequential digital circuits are presented. The steps of this transform from biologics to logic involve the enzymes 'electron kinetic behavior, which reveals the basic reaction pathways of the enzyme building blocks. Because these pathways are well defined, with each enzyme going through several different conformations, each conformation can be defined in terms of a logic state. The definitions can be used to describe a state machine for the enzyme building block.

Molecular Computing: The Lock-Key Paradigm ( Michael Conrad ; IEEE Computer Magazine 1992-11)

- Molecular computers are natural or artificial systems in which macromolecules individually mediate critical information-processing functions. Biological organisms are the naturally occurring examples. Their information-processing virtuosity traces ultimately to the fact that macromolecules, most notably proteins, can recognize specific molecular objects in their environment in a manner that uses shape and depends sensitively on physiochemical context. The ultimate capabilities of this shape-based mode of computing and the technological implications that this mode may have are discussed. Basic principles of molecular computing are introduced and some ways that they might combine to yield new approaches to information technology are considered. Specifically, signal-integrating, optomolecular and neuromolecular computer architectures are described.

Understanding Diagrams in Technical Documents ( Robert P. Futrelle, Ioannis A. Kakadiaris, Jeff Alexander, Catherine M. Carriero, Niko Nikolakis, Joseph M. Futrelle ; IEEE Computer Magazine 1992-07)

- The development of a knowledge base of biological research papers that supports the Scientist's Assistant, an intelligent system that will provide a scientist with interactive access to the research results, methods, and reasoning in a collection of scientific papers, is discussed. The document understanding system uses graphics constraint grammars for describing and analyzing diagrams, spatial indexing in diagram analysis and understanding, and extension of natural-language processing techniques to complex scientific text. The graphics constraint grammars of the diagram-understanding system are described in detail. Example diagrams and grammars are presented.

(Partial list shown.)
[Complete List of Articles]

Questions and Answers: Showing

Linux and Biometrics? [2002/03/04]

At Ask Slashdot

What Science/Bioinformatics Magazines Do You Read? [2001/12/13]

At Ask Slashdot

Bioinformatics Books for the Technically Inclined? [2001/12/07]

At Ask Slashdot

Linux And Biometrics (Redux)? [ 2000/10/18]

At Ask Slashdot

DNA Repositories? [ 2000/09/08]

At Ask Slashdot

Unix Software for Molecular Biology? [ 2000/04/23]

At Ask Slashdot

Learning About Genetic Engineering On The Net [ 2000/03/12]

At Ask Slashdot

Distributed Computing and the Human Genome Project [ 1999/11/22]

At Ask Slashdot

Questions and Answers

Others not displayed here
Full List

Applications and Utilities: Showing

Gisk - This package is intended to control dilutions of proteins / lipids / detergents mixtures in a reproducible, easy and even fun way in order to produce protein cristals. {(L)GPL}

At Sourceforge ( Production/Stable)

fluctuate-1.30 - A program to fit population models

At FreeBSD Ports

migrate-1.2.4 - A program to estimate population sizes and migration rates

At FreeBSD Ports

dna-qc-1993.07.26 - A quality control algorithm for DNA sequencing projects

At FreeBSD Ports

artemis-4.0 - A DNA sequence viewer and annotation tool

At FreeBSD Ports

crimap-2.4 - Creation of multilocus linkage maps

At FreeBSD Ports

gff2ps-0.97b - Converts gff-formated genomic data-sets to PostScript

At FreeBSD Ports

coalesce-1.50 - A program to fit population models

At FreeBSD Ports

nclever-4.0 - NClever is a character-based version of NCBI's Entrez program

At FreeBSD Ports

grappa-1.0.3 - Genome Rearrangements Analysis and Phylogeny Software

At FreeBSD Ports

ja-lsd-fpw-3.0 - A Japanese - English Dictionary for Life Science (EPWING V1 format)

At FreeBSD Ports

lamarc-2001.08.06 - A package of programs for computing population parameters

At FreeBSD Ports

nab-4.3.2 - This is nab (nucleic acid builder), a language for macromolecules

At FreeBSD Ports

phylip-3.6 - A Phylogeny Inference Package

At FreeBSD Ports
phylip-3.573c - Phylogeny Inference Package (At NetBSD packages collection)

biojava-1.01 - Open-source java tools for processing biological data

At FreeBSD Ports

clustalw-1.82 - CLUSTAL W Multiple Sequence Alignment Program

At FreeBSD Ports
clustalw-1.8 - General purpose multiple alignment program for DNA or proteins (At NetBSD packages collection)

fasta-20.u66 - A collection of programs for searching DNA and protein databases

At FreeBSD Ports

fasta3-33.t08.d4 - A collection of programs for searching DNA and protein databases, v3

At FreeBSD Ports

genpak-0.26 - GP is a set of small utilities to manipulate DNA sequences

At FreeBSD Ports

p5-AcePerl-1.82 - Perl5 interface to the ACEDB genome database system

At FreeBSD Ports

sim4-2001.12.30 - An algorithm for aligning expressed DNA with genomic sequences

At FreeBSD Ports

paml-3.1 - Phylogenetic Analysis by Maximum Likelihood (PAML)

At FreeBSD Ports

fastdnaml-1.2.2 - The faster variant of DNAML, makes phylogenetic trees using maximum likelihood

At FreeBSD Ports
fastDNAml-1.2.1 - Program derived from Joseph Felsenstein's version 3.3 DNAML (At NetBSD packages collection)

ecg2png-0.30_1 - Converts scanned 12-lead electrocardiograms into PNGs

At FreeBSD Ports

emboss-2.2.0 - A collection of open source tools for genetic sequence analysis

At FreeBSD Ports

ortep3-1.0.3_2 - The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure

At FreeBSD Ports

p5-bioperl-devel-0.9.0 - A collection of Perl modules for bioinformatics (developer's release)

At FreeBSD Ports

recombine-1.40 - A program to fit population models across sites

At FreeBSD Ports

ruby-bio-0.3.6 - Integrated environment for Bioinformatics written in Ruby

At FreeBSD Ports

seqio-1.2.2 - A set of C functions which can read/write biological sequence files

At FreeBSD Ports

spdbv-37b2 - Deep View Swiss-PdbViewer is a Protein viewer and analysis tool

At FreeBSD Ports

tRNAscan-SE-1.21 - An improved tool for transfer RNA detection

At FreeBSD Ports

t_coffee-1.37 - A multiple DNA or protein sequence alignment package

At FreeBSD Ports

hmmer-2.2.g - Profile hidden Markov models for biological sequence analysis

At FreeBSD Ports

kinemage-5.79 - A molecular visualization program with special functions

At FreeBSD Ports

povchem-1.0_1 - Simple yet powerful tool to generate POV from a PDB file

At FreeBSD Ports

rasmol-2.7.2 - Fast Molecular Visualization Program

At FreeBSD Ports
rasmol-2.7.1 - Molecular Graphics Visualisation Tool (At NetBSD packages collection)

seaview-1.0 - Multiple DNA sequence alignment editor

At FreeBSD Ports

tinker-3.9_1 - A general purpose molecular modelling package

At FreeBSD Ports

treeviewx-0.2 - A phylogenetic tree viewer

At FreeBSD Ports

WEEDS - Java application that converts XML files describing plants into an HTML flora {Artistic}

(Info at freshmeat)

Dinosaurs Pocket Edition

Dinosaurs: Lifestyles of the Big & Carnivorous (Jewel Case)

The Ultimate Birder

Kaplan Biology And Chemistry Essential Review

The Living Oceans (4 CD-ROM)

The Oceans 3 CD-Rom Set (Jewel Case)

Birds: Cranes through Passerines (Jewel Case)

High School Biology

Birds of the World

Applications and Utilities

Others not displayed here
Full List

Libraries and Components: Showing

p5-bioperl-0.7.2 - A collection of Perl modules for bioinformatics

At FreeBSD Ports

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