Bioinformatics Web Log
Last updated
May 21, 2001
Questions, comments,
suggestions?
-
Clustering
- BCI
Hierarchical Agglomerative Clustering Pac...
- Hierarchical Agglomerative Clustering (Barnard and Downs,
1992; Downs and Willett, 1994; Barnard and Downs, 1997) involves
building a hierarchical classification of compounds in a dataset
by a series of binary mergers (agglomerations), initially
of indivi
- Cluster
Analysis and Display of Genome-wide E...
- Clustering
Global Optimization Methods
- Clustering global optimization methods can be viewed as
a modified form of the standard multistart procedure, which
performs a local search from several points distributed over
the entire search domain. A drawback of Multistart is that
when many starting
- Clustering
Methods
- Most of the existing approaches to document clustering are
based on either probabilistic methods, or distance and similarity
measures (see [FBY92]). Distance-based methods such as k-means
analysis, hierarchical clustering [JD88] and nearest-neighbor
clust
- Clustering
Methods:
- Sequences are clustered into subalignments by using a similarity
measure [33,34,26]. The clustered subalignments are subsequently
aligned to one another by employing various consensus methods
that reduce each subalignment to a single consensus sequence.
E
-
Databases
- A
Cross-Comparison of a Large Dataset of Genes
- Alu
and RAREs & TREs
- Homeobox Genes DataBase ,
Phylogeny and Evolution, Alu and RAREs & TREs
- BCM
Human Transcript Database Home Page
- The Human Transcript Database (HTD) is a curated source
for information related to RNA molecules that have been sequenced.
The goal of the HTD is to provide a clone-based platform that
represents as many of the human transcripts that have been
sequenced a
- Database
NCBI
-
- EBI
MSD Database System Schema
- The EBI Macromolecular Structure Database is the European
Project for the collection, management and distribution of
data about macromolecular structures.
- Entrez-Genome
- Entrez-PopSet
- Population Specific Data
- Entrez-Protein
- Entrez-PubMed
- Entrez-Structure
- ETH:
CBRG Server - SwissProt Analysis
- AllAllDB: Querying the all-against-all database of SwissProt
* MassSearch: Searching SwissProt or EMBL by protein mass
after digestion * NuclPepSearch: Searching SwissProt for
a nucleotide sequence (Sorry! This service currently unavailable)
* PepPepSearc
- Human
Genome Working Draft
- This page contains links to an assembly of the current draft
of the human genome. The human genome is approximately 3.2
billion bases. More than 90% of the genome has been sequenced
by the International Human Genome Project, and approximately
88% is inclu
- MGI
Home Page
- MSD
Home
- The EBI Macromolecular Structure Database is the European
Project for the collection, management and distribution of
data about macromolecular structures.
- OMIM
Home Page -- Online Mendelian Inheritan...
- Protein
Information Resource Home Page - Prot...
- The Protein Information Resource (PIR), in collaboration
with the Munich Information Center for Protein Sequences (MIPS)
and the Japanese International Protein Sequence Database (JIPID)
maintains the PIR-International Protein Sequence Database
--- a compr
-
-
- The
I.M.A.G.E. Consortium
- World's largest publiuc collection of genes. (There are
some software tools here too)
-
-
DB Tools
- Data
Management Tools
- Java
- Oracle Corporation
- Mac
ODBC Guide
- Papers
on Developing Database Systems and Dat...
-
Schemas
- ASN.1
Summary
- ASN.1, or Abstract Syntax Notation One, is an
International Standards Organization (ISO) data representation
format used to achieve interoperability between platforms.
NCBI uses ASN.1 for the storage and retrieval of data
such as nucleotide and protein s
- DDBJ/EMBL/GenBank
Feature Table DefinitionDDB...
- DNA
Sequence Collaborator's Page
- International Nucleotide Sequence Database Collaboration
- Ensembl
Genome Server Schema
- GDB
Schema Documentation
- The
OPM Project
-
Emerging Standards in Bioinformatics
-
Perl
- bio.perl.org
- The Bioperl Project is an international association
of developers of open source Perl tools for bioinformatics,
genomics and life science research. We work closely with
our friends and colleagues at biojava.org, biopython.org,
bioxml.org and biocorba.org.
- Mother
of Perl - WebReference.com
- www.perl.com
- Report from the Perl Conference
- AppLab
Homepage
- CORBA-Java based Application Wrapper
- Applab
Homepage
- A CORBA interface to the command-line driven programs
(with primary concern on biosequence analysis tools in
bio-informatics) AppLab's main goal is to develop a distributed
object system, which provides an easy-to-use and well-defined
access to a large
- Bruce
Eckel's MindView, Inc. OOP Resources
- CORBA
Distributed Objects For Biological Databa…
- BioORB - BioCORBA
- Ensembl
Genome Server
- Ensembl is both code (software) and data. The code is predominantly
Perl at the moment (but we don't expect that to last in the
long term. There is alot of talk for moving to Java for new
projects, probably in the Fall 2000, with CORBA coming into
play fo
- Functional
Genomics - The Next Big Step
- After years of trying to understand gene function, scientists
grasp the role of only a minority of genes. With traditional
tools, investigators could look at no more than a handful
of genes at a time. In the wake of genome sequencing projects,
however, th
-
JAVA and JAVAscript
- Apple
Developer - MRJ Software Download
- Mac OS Runtime for Java (MRJ) 2.2.2 is Apple's implementation
of the Java Virtual Machine (JVM), based on Sun Microsystems'
Java 1.1.8 specification. MRJ provides the runtime software
needed to run Java applets and applications, and the Apple
Applet Runne
- Cut-N-Paste
JavaScript
- Featuring more than 200 FREE JavaScripts you can simply
paste into your HTML
- Download
JDesignerPro for any platform
- JDesignerPro is a rapid application development and
deployment system specifically designed to help you build
database driven applications that run on any browser or
wireless handheld device with no programming experience
necessary
- Java/CORBA
tools
- A collection of freely available tools for CORBA and Java
developers, distributed with source code and documentation.
- JavaBeans(TM)
- JavaBeans component architecture is the platform-neutral
architecture for the Java application environment. It's the
ideal choice for developing or assembling network-aware solutions
for heterogeneous hardware and operating system environments--within
the
- Open
BSA - Biomolecular Sequence Analysis
- Biomolecular Sequence Analysis is the first (together with
Genomic Maps) standardized and adopted technology by Life
Science Research Domain Task Force (LSR) within Object Management
Group (OMG). The specification is the result of a joint submission
of bo
- Parabon
Computation, Inc. -- Internet Computation
- When you're not using your computer, its power is simply
being wasted. By running Pioneer™, you connect with
computers worldwide to create a massive computer, capable
of solving computing problems in areas such as cancer research
and digital animation.
- Protein
Function and Metabolic Pathways
- Simple
Object Access Protocol (SOAP) 1.1
- SOAP is a lightweight protocol for exchange of information
in a decentralized, distributed environment. It is an XML
based protocol that consists of three parts: an envelope that
defines a framework for describing what is in a message and
how to process i
- The
Open Lab: About The Open Lab
- The Open Lab is a not-for-profit foundation established
to sponsor open collaborations in research and software development
in the scientific field of computational biology. We
stand firmly on our conviction that science is for the sake
of science and no
-
XML
- bio.xml.org
- bioxml.org is a resource to gather XML documentation,
DTDs and tools for biology in one central location.
It overlaps in interest and in tools with the BioPerlproject,
which also hosts a page about XML. Our goal is to
provide the biology community with
- Mac
Web Servers: Serving Up XML
- Flushing out some of the lesser-known XML-related applications
for the Mac.
- Welcome
to Extensibility
- XML Development tools
- Working
with XML: The Java(TM)/XML Tutorial
- he JavaTM XML Tutorial, is an online manual that can
quickly get you up to speed writing XML code and XML-based
software for end-user applications. Using step-by-step
walkthroughs and lots of code examples, the Tutorial is
divided into three major parts t
- XML
- Oracle Corporation
- XML
Linking Language (XLink)
- This specification defines the XML Linking Language
(XLink), which allows elements to be inserted into XML
documents in order to create and describe links between
resources. It uses XML syntax to create structures that
can describe links similar to the si
- XML.ORG
- The XML Industry Portal
- The XML.ORG Registry is a community resource for accessing
the fast-growing body of XML specifications, schemas and
vocabularies being developed for vertical industries and
horizontal applications. It is designed to foster collaboration
and enhance commun
-
EST
- EST
@ EBI: JESAM
- The JESAM package is used at the EBI to build the alignments
and clusters of the EuroGeneIndexes. The software is based
on the ICAtools (Parsons, J.D., Brenner, S. and Bishop, M.J.,
(1992), Clustering cDNA Sequences, Comput. Applic. Biosci.,
8, 461-466 an
- SA
National Bioinformatics Institute
-
Gene Finding
- Bioinformatics,
Volume 15, Issue 11, pp. 874-...
- WebGene
Home Page
-
General Info
- BioABACUS
Search
- BioABACUS is a searchable database of abbreviations and
acronyms in Biotechnology that contains terms in such categories
as: Biochemistry, Cell Biology, Computers and Internet, Diseases,
Grants, Journals, Laboratories, Medicine, Molecular Biology/Genetic
- Bioinform
- The Global Bioinformatics News Serv…
- Bioinformatics Global News Service
- Bioinformatics
News Service
- BiologyJobs.com
- A targeted resource for the...
- BiologyJobs.com was created as a targeted resource for job
seekers and employers who are specifically interested in the
Life Sciences. Biology Job categories in our database include
Agriculture, Anatomy / Physiology, Bioinformatics / Biotechnology,
Botany
- BioMedNet
List of Conferences
- Biotech:
Bioinformatics
- General info from the University of Texas
- CAS
General Subject Vocabulary Helper
- Chemical Abstrcts Hyper Dictionary
- CMP243
Home Page
- A bioinformatics class @ UCSC
-
Companies
- ACLARA
BIOSCIENCES
- Microfluid Array Devices for Genomics and Pharmaceutical
Drug Screening
- Biotechnology
Company Registry
- DigiScents,
Inc.
- GCG
(Genetics Computer Group)
- InforMax
Inc.
- Orchid
- A leader in genetic diversity.
- SNP-IT, SNP Identification Technology
- Documentation
and Bioinformatics Courses
- This is a collection of documentation and courses on bioinformatics
topics.
-
Ethics
- Turning
Their Genes Into Green
- Residents of Framingham, Massachusetts, donated their
private health data in the name of science 52 years ago.
Should a genomics company be allowed to profit from the
heart disease studies?
-
General Reference
- Amazon.com
Listmania Results
- Bioinformatics & Computational Biology Essentials
by Cynthia Gibas, computational biologist
- BioExchange
- BioMedNet
- Bioplanet
Home Page
- Bioinformatics articles, jobs, links, etc.
- Science
Next Wave Global Home
- NextWave, the weekly on-line publication devoted to
scientific training and career development, provides global
news, profiles of emerging careers, and advice from experts
and role models drawn from your international scientific
community
- SCIENTIFIC
COMPUTING: AN INTRODUCTORY SURVEY
- WebReference.com
- The Webmaster's Reference ...
- Google
Web Directory - Science > Biology
-
Interesting
- G
E N E H A C K:weblog
- Genomics:
Legislation and Regulation
- InGenuity.com
- Myhrvold:
Genomics Will Rule
- Starring
role in Genome Project, 02-12-01
- Graduate student lands starring role in the Human Genome
Project. New York Times profile of Jim Kent They may as
well go ahead and give Jim Kent his Ph.D. now, considering
his role in a scientific achievement destined for the
history books. Kent, a gradua
- Intro
to Bioinformatics Course Material Index
- Principles of Protein Structure Using the Internet @ Birkbeck
College
-
Investing
- Google
Web Directory - Science > Biology > Business
- International
Biotechnology Trust
- The UK's first international biotechnology investment
trust
International Biotechnology Trust plc (IBT) is the
UK's first approved investment trust dedicated to the
biotechnology sector. It offers investors the means
to invest in a carefully selected and
- Welcome
to GenomeWeb -- New Media for the New Biology
- GenomeWeb is a growing print and electronic provider
of news and information on the business and technology
of
genomics and bioinformatics worldwide. GenomeWeb’s
customers include research enterprises in the pharmaceutical,
agriscience, biotechnology,
-
Jobs and Postdoctoral Opportunities
- HUM-MOLGEN:
Positions in Bioscience and Medicine
- Way2Goal:
Postdoctoral Web Sites
- Links2Go:
Bioinformatics
- A cool links page of Bioinformatics resources
- Welcome
to Biotaq.com - Biotechnology informa...
- Biotaq.com is a dynamic data-driven web site containing
extensive links to valuable biotech resources and up-to-date
industry and corporate information. We are dedicated to provide
a high quality biotech Internet information services to the
biotechnology
-
Institutes and Research Groups
- Arizona
Biotechnolgy Computing Facility
- Tutoring, workshops, how-to's, tools, software
- Center
for Computational Biology - MSU
- Computational
Biology at UC Santa Cruz
- Department
of Molecular Biotechnology
- University of Washington
- EBI,
the European Bioinformatics Institute
- The EMBL Outstation - European Bioinformatics Institute
(EBI) is a centre for research and services in bioinformatics.
The Institute manages databases of biological data including
nucleic acid, protein sequences and macromolecular structures.
- Ensembl
Genome Server
- Ensembl is a joint project between EMBL-EBI and the Sanger
Centre to develop a software system which produces and maintains
automatic annotation on eukaryotic genomes. Human data are
available now; worm and mouse will be added soon
- ETH:
Computational Biochemistry Research Group
- Forsdyke
Laboratory
- Queens University, Canada. Molecular Biology and Bioinformatics
- [ keywords: G0/G1 switch genes (G0S genes), Cell Cycle,
Lymphocytes, Immunology, Bioinformatics, Genomics,
Theoretical Biology, Speciation, Evolution,
Darwin, Romanes, Bateson.]
- Human
Genome Project Research in Progress
- MBL Home
- Marine Biological Laboratory - Woods Hole, Mass.
- Montreal
Genome Centre Homepage
- National
Human Genome Research Institute (NHGRI)
- RSBS
Bioinformatics Group homepage
- Australian National University
- Stein
Laboratory
- This is a Web site run by Lincoln Stein at Cold Spring Harbor
Laboratory in Cold Spring Harbor, NY. My laboratory develops
software for computational biology and genome bioinformatics.
Main areas of current research are pointed to by the navigation
bar ab
- Stockholm
Bioinformatics Center
- The
Swiss Institute of Bioinformatics
- The
UCSC Center for Biomolecular Engineering
- Theoretical
Biophysics Group Home Page
- NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
- UCLA
Bioinformatics
-
Journals and Publishers
- Birkhäuser
Boston
- Scientific and Technical Publishing in Mathematics - Physics
- Biology - Biomedical Sciences - Computer Science - Engineering
- Architecture
- Clinical
Chemistry
- Genome
Research
- The journal focuses on genome studies in all species, and
presents research that provides or aids in genome-based analyses
of biological processes. The journal represents a nexus point
where genomic information, applications, and technology come
together
- Nature
Genome Information Centre
- Welcome to Nature's Genome Gateway, a comprehensive web
resource devoted to genomics. Access is free and the Gateway
provides: * A library of original research papers, including
all genome-related papers from Nature and Nature Genetics
plus links to other
- PROW,
Protein Reviews on the Web
- Protein Reviews On the Web is an online resource that features
PROW Guides, authoritative short, structured reviews on proteins
and protein families. The Guides provide approximately 20
standardized categories of information (abstract, biochemical
functio
- Scientific
American
- World
Scientific Online Bookshop
-
Mass Spec
-
Meetings and Conferences
- Bioinformatics
2001
- Bioinformatics 2001 is the third major international bioinformatics
meeting in Scandinavia. It is organized jointly by bioinformatics
groups from the Nordic countries, and aims to cover current
developments in research on all aspects of bioinformatics.
B
- EMO'01
Conference
- First International Conference on Evolutionary, Multi-Criterion
Optimization, March 7-9, 2001, Zurich, Switzerland
- International
Conference on Data Engineering
- Linkage
Disequilibrium Mapping Meeting
- RECOMB
2001
- The conference series aims at attracting research contributions
in all areas of computational molecular biology. Typical,
but not exclusive, the topics of interest are genomics, molecular
sequence analysis, recognition of genes and regulatory elements,
mo
- SAC
2001
- SAC 2001 Call for Papers
16th ACM Symposium on Applied Computing
March 11-14, 2001
Las Vegas, USA
-
Microarrays, Proteomics, and More
Post-Genomics
- Gene
Expression Omnibus Home
-
In order to support the public use and dissemination of
gene expression data, NCBI has launched the Gene Expression
Omnibus. GEO is our effort to build a gene expression data
repository and online resource for the retrieval of gene
expression data from
- genome
gateway > post-genomics
- The genome has been sequenced, the paper published, the
champagne polished off. Now what? These pages focus on some
of the developments of science in the post-genome era.
The chipping forecast: A special supplement from Nature
Genetics which provides an
- IPAM
Function Genomics Program
- Knowledge-based
Analysis of Microarray Gene E...
- We introduce a new method of functionally classifying genes
using gene expression data from DNA microarray hybridization
experiments. The method is based on the theory of support
vector machines. SVMs are considered a supervised computer
learning method b
- Microarrays,
their application and the standa...
- MicroArray Informatics at the EBI: Projects ,* Expression
Profiler ,a Web-based tool for microarray data analysis ,*
Microarray Data Standardisation ,an international effort to
adopt microarray data and annotation standards , * ArrayExpress,
a public re
- NHGRI
Microarray Project: Home Page
- papers
on microarray data analysis
- This is a collection of papers with emphasis on analysis
of microarray (a.k.a. DNA chip) data. General reviews on microarray
are occasionally included. Analysis of gene network is also
occasionally included. However, papers on microarray technology
itself
- Peter
Lee's Website at the Montreal Genome Ce...
- Working with the Expression Informatics Group at the Montreal
Genome Centre. We are interested in the combination of Functional
Genomics and Computational Techniques in deciphering questions
of genetic control. This project is a joint effort with the
McGi
- Research
seminar on statistics of gene expres...
- Scientific
American: Technology and Business...
- Shrinking to Enormity
DNA microarrays are reshaping basic biology--but scientists
fear they may soon drown in the data
- Signal
Transduction Knowledge Environment
- Science Mag and Stanford University Web Page with protocols,
perspectives, reviews, and related info to this topic.
- Silicon
Genetics: gene expression software
- Silicon Genetics is a leading provider of software solutions
for genomic expression analysis experiments.
- Software
for MicroArray Gene Expression Analysis
- I have tested several PC based software packages for the
analysis of microarray data. All packages were demonstration
versions with limited file load/save/print capability and/or
a time-limited license, except ScanAlyze, Cluster and TreeView
from Stanford
- Statistical
problems involving microarray data
- U.S.
Environmental Protection Agency Microarr...
- forum for collaboration in the development and application
of microarray technology for gene expression analysis in a
number of model systems. The consortium was instigated by
the Reproductive Toxicology Division (RTD) of the National
Health and Environm
- UCLA
Bioinformatics
- Web
resources on Gene Expression and DNA Micr...
- This site is a collection of web resources and pointers
to information on large-scale gene expression studies, and
especially microarray technologies. The links included are
biased towards the development and applications of informatics
and bioinformatics
- Welcome
to Speed's Microarray Homepage
- What are we offering? Our hope is that we can identify simple
and reliable solutions to the statistical problems met
in day to day microarray data analysis, and refer you to them.
Some of these will be our own work; much will be from others.
Where possi
-
More Links
- Bioinformatics,
biocomputing: Biotaq.com
- Biotaq.com is a dynamic data-driven web site containing
extensive links to valuable biotech resources and up-to-date
industry and corporate information. We are dedicated to provide
a high quality biotech Internet information services to the
biotechnology
- Biolinks
- Links to: Tutorials and Educational Resource, Employment,
Bioinformatics Servers and Home Pages, Sequence Databases
and Searching, Sequence Databases, Sequence Searching, Misc
Search Tools, Sequence Analysis, Analysis Tools, Alignment
Tools, Sequence Fami
- Computational
Biology or Bioinformatics references
- ETH: CBRG
- Search
- Molecular
Biology Information Servers/BioInfo...
- US Dept Commerce/NOAA/NMFS/NWFSC, Bioinformatics: Biology
and Molecular Biology Resources
- Molecular
Evolution, Organelle Genomics & Genome Bioinformatics Resources
- Univerity Montreal
- Nature
Net Guide
- This is the first in a series of quarterly Net Guides being
produced by the Nature group, each of which will sample the
best of what the web has to offer in a couple of scientific
disciplines, based on recommendations from Nature's staff
and other experts
- oligo
program links
- Sequence
Alignment References
- Tel
Aviv University Bioinformatics Unit
- Bioinformatics Unit, G.S. Wise Faculty of Life Sciences,
Tel-Aviv University, Israel, Sites Relevant to Bioinformatics
Users
- The
Genetic Algorithms Archive
- The Genetic Algorithms Archive is a repository for information
related to research in genetic algorithms and other forms
of evolutionary computation. Available from this site are
past issues of the GA-List digest, source code for many GA
implementations,
- yfleung's
functional genomics home
-
Multiple Sequence Alignment
-
MSA Info
- The
Statistics of Sequence Similarity Scores
- To assess whether a given alignment constitutes evidence
for homology, it helps to know how strong an alignment
can be expected from chance alone. In this context, "chance"
can mean the comparison of (i) real but non-homologous
sequences; (ii) real sequen
-
Software
-
Personal Pages
- Ari
Kahn's Home Page: ETH
- Computational Biology, Bioinformatics, BioOpera, Darwin,
Phylogenetics, Physiological Ecology, Grasses, Crustaceans,
Macintosh, CBRG Server
- Gaston
H. Gonnet personal pages
- Symbolic and algebraic computation, in particular solving
equations (symbolically and numerically), system development,
limit and series computation and heuristic algorithms. Co-founder
in 1980 of the Symbolic Computation Group at the University
of Waterl
- Genetics
in Motion
- Michael Mann - SNP, Links, Cancer
- Marcel
Turcotte
- I study the complex relationships that exist between sequence,
structure and function. Over the next five years, I intend
to develop the followings three axes: 1. New models for sequence
comparison. Increase in both computer processing power and
amount o
- Mike
Hallett
- Hard core phylogenetic algorithms!
- Xianghong
Zhou's Homepage
- Research Interests: Microarray analysis / Expression profiling,
Protein structure, Prediction of protein secondary structure
using the singular value decomposition, The relationship between
peptide sequences and their secondary structure, Protein folding
-
Phylogenetics
- Benno
Schwikowski - Research in Computational...
- Our goal is to develop new methods for the reconstruction
of phylogenetic trees from molecular data. An established
principle for reconstructing evolution from molecular data
is Parsimony. Parsimony guides the search for an explanation
of the given sequen
- Cladistics
- Speciation Model
- Comparative
Evolutionary Analysis of Mitochondrial Genomes Using Maximum
Likelihood
Comparative Evolutionary Analysis of Mitochondrial Genomes
Using Maximum Likelihood
Comparative Evolutionary Analysis of Using Maximum Likelihood
- Analysis of Mitochondrial Genomes
- ETH:
CBRG - Research
- BioOpera, Darwin, MSAs, Phylogentics, Algorithms, publications
- Introduction
to Phylogeny
- Molecular
Phylogenetics and Evolution
- MPL
- Molecular Phylogenetics Lab at UC Berkeley
- NEE-HOW:
Databases- phylogenetics/ taxonomy
- Oxford
University Evolutionary Biology Group
- This is a site for various projects in evolutionary biology,
molecular evolution and phylogenetic epidemiology being carried
out by members of the research group headed by Paul Harvey
in the Department of Zoology at the University of Oxford.
- Parsimony
Tree Generator
- Phylogenetic
Analysis
- Phylogenetics
Resources
- Phylogeny
and Evolution
- PPS
96' - Molecular Phylogenetics
- Systematic
Biology Home Page
- University of Texas
- Web
Resources in Molecular Evolution and Systematics
- Univerity of Conneticut
- Western
Palearctic Water Frogs + Water Frog I...
-
Servers
- Arizona
BCF: Stand-Alone Convert
- Convert your "single" sequence from one format to another.
- Bioinformatics
Servers
-
BioSystems and Tools
- LabOnWeb
- LabOnWeb.com is the first life science research engine,
a collection of gene discovery tools designed to accelerate
work in the lab, improve the quality and accuracy of experiments,
simplify the delivery of information and help researchers
make more infor
- Bio-OPERA
- The goal of Bio-OPERA is to provide the computational
biologist with a platform that takes care of all data
handling and record keeping chores so that the user can
concentrate on the biology aspect while the system takes
care of the book keeping necessary
- GeneQuiz
II: a system for sequence analysis
- GeneQuiz is an integrated system for large-scale biological
sequence analysis, that goes from a protein sequence to
a biochemical function, using a variety of search and
analysis methods and up-to-date protein and DNA databases.
Applying an "expert system
- LabBook.com
- Provides XML powered internet and bioinformatic applications
for the life sciences
- PAPIA
: PArallel Protein Information Analysis s…
- We aim to demonstrate the power of parallel calculation
technology by efficiently solving computational biology
problems. For this purpose, we have developed the PAPIA
(PArallel Protein Information Analysis) system.
- www.doubletwist.com
- DoubleTwist.com is an integrated genomics portal that
provides a secure and comprehensive technology platform
to simplify and accelerate life science discovery. Our
research agents provide you with easy, point-and-click
bioinformatics capabilities and acc
- DeepForest
- Environment for studies of molecular evolution: Powered
by KL1/KLIC
- ExPASy
Molecular Biology Server
- This is the ExPASy (Expert Protein Analysis System) proteomics
server of the Swiss Institute of Bioinformatics (SIB). This
server is dedicated to the analysis of protein sequences and
structures as well as 2-D PAGE (Disclaimer).
- Felsenstein's
Phylogeny Programs
- Web or e-mail servers that can analyze data for you
- Logiciels
pour la biologie installés sur central
- Run ProtML, NucML and NJDist phylogeny programs with your
data.
- Molphy
(Phylogenetic Analysis Package)
- SeWeR:
Sequence Analysis using Web Resources
- What is SeWeR? SeWeR is an acronym, stands for SEquence
analysis using WEb Resources. In addition to its common *dirty*
use, the word SeWeR also has two meanings- first, "a medieval
servant or household officer of high rank in charge of serving
the dishe
- SplicePredictor
Online
- a method to identify potential splice sites in (plant) pre-mRNA
by sequence inspection
- SWISS-MODEL
- SWISS-MODEL is an Automated Protein Modelling Server running
at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
The purpose of this server is to make Protein Modelling accessible
to all biochemists and molecular biologists World Wide. The
- UCLA
Bioinformatics Servers
- The UCLA-DOE Fold Recognition Server, Verify 3D Crystal
Structure Verification Server, Errat Crystal Structure Verification
Server, Micro Array Database Server, RNA Editing Websitte,
Uridine Insertion/Deletion Home, Uridine Insertion/Deletion
Database
-
Software
-
ftp Servers
- Indiana
U ftp server
- This is a user-supported archive for biology software
and data
- Sanger
UK ftp server
-
Other
- Biology
Software for Windows NT
- DNASIS
software
- DNA / RNA Analysis and Protein Analysis Package
• Custom plasmid map drawing
• Circular and linear restriction maps
• Customized enzyme tablets and selection criteria
• Primer design
• RNA folding
• ORF analysis
• Contig manager (automatic and manual frag
- EMBOSS
Homepage
- EMBOSS is a new, free Open Source software analysis
package specially developed for the needs of the molecular
biology (e.g. EMBnet) user community. The software automatically
copes with data in a variety of formats and even allows
transparent retrieval o
- ETH:
CBRG - DARWIN's Home
- Darwin v. 2.0 , an interpreted computer language especially
tailored to researchers in the biosciences. The system
is a general tool applicable to a wide range of problems.
This second release improves Darwin version 1.6 in several
ways: it now contains (
- Freely
distributable documents and computer p...
- GCG
Products and Services
- Data Management and Sequence Analysis
SeqStore (relational, Oracle based)
Sequence Analysis
GCG Wisconsin Package (UNIX)
MacVector (Macintosh)
OMIGA (Windows 95/98/NT systems)
Interfaces to the GCG Wisconsin Package
SeqWeb (web intranet)
SeqLab (X Window
- http://iubio.bio.indiana.edu/...io/Listings.html
- Free Software in Molecular Biology for Macintosh and
MS Windows computers
- IBM
techexplorer Hypermedia Browser
- IBM techexplorer is a plug-in for Navigator and
Internet Explorer and an ActiveX control for applications
like Microsoft PowerPoint and Word. techexplorer enables
the display of TeX, LaTeX and MathML documents and the
publishing of interactive scientifi
- Linux
Bioinformatics Software
- The
BioOpera Homepage
- BioOpera is a joint project between the Information
and Communication Systems and the Computational Biochemistry
Research Group (CBRG) at the Swiss Federal Institute of
Technology in Zurich. Our goal is to improve and automatize
large scale analysis of ge
- Unix
Bioinformatics Software
- Waterloo
Maple: Home
-
Phylogenetics Software
- Debian
GNU/Linux -- fastdnaml
- fastDNAml is a program derived from Joseph Felsenstein's
version 3.3 DNAML (part of his PHYLIP package). Users
should consult the documentation for DNAML before using
this program. fastDNAml is an attempt to solve the same
problem as DNAML, but to do so f
- ISMLIB
Other Software
- MOLPHY/ProtML - uses Maximum Likelihood with protiens
- LAMARC
- estimating population parameters
- a package of programs for computing population parameters,
such as population size, population growth rate and migration
rates by using likelihoods for samples of data (sequences,
microsatellites, and electrophoretic polymorphisms) from
populations. It ap
- PAUP*
4.0
- PHYLIP
Home Page
- PHYLIP is a free package of programs for inferring phylogenies.
It is distributed as source code, documentation files,
and a number of different types of executables. These
Web pages, being constructed by Joe Felsenstein of the
Department of Genetics at t
- Phylogenetic
Analysis by Maximum Likelihood (...
- Phylogeny
Programs
- Here are some 175 of the phylogeny packages, and 17
free servers, that I know about. Some of them are available
over Felsenstein's Phylogeny Program List: Internet from
ftp server machines, or by World Wide Web. The programs
listed below include both fre
- PROTML:
Maximum Likelihood Inference of Prote...
- T-REX
(Tree Reconstruction)
- TrExML
Information
- TrExML is a program derived from Olsen et al.'s fastDNAml.
Whereas fastDNAml was written to be a fast program for
inferring phylogenetic relationships and comparing evolutionary
hypotheses, TrExML is written to provide a more exhaustive
coverage of evolut
-
Scientific Computing
-
Sequence Analysis Software
-
Viewing Software
- VMD
- Visual Molecular Dynamics
- NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
-
Structures
- 3D
ALI PAGE
- A DATABANK (3D_ali) COLLECTING RELATED PROTEIN SEQUENCES
AND STRUCTURES
-
Courses
- Algorithms
in Molecular Biology, Fall 1998-99
- Tel Aviv University Department of Computer Science, Ron
Shamir
- Applixware
Presentation
- First International Bioinformatics Summer School 1999 (IBSS'99)
Presentation Slides
Overview, Classical Clustering Methods, Classical clustering,
an example, Mixture Models based Applications, The Mixture
Models Classification Approach, BClass Scheme, MCM
- Biocomputing
Course Resource List : Course Syllabi
- Biocomputing
Course Resource List : Course Syllabi
- Bioinformatics
at Queens University, Canada
- Bioinformatics:
Online Courses
- The development of bioinformatics courses is still in its
infancy. Only a few universities around the world offer courses
specifically designed for this field. Following are the few
online courses in bioinformatics currently accessible, two
of which repre
- Computational
Biology Course @ ETH ad McGill
- This course focuses on the application of computer
science
techniques to problems arising in biology and biochemistry.
We will present mathematical models of evolution, discussions
about the role bioinformatics will play in the future of
drug design,
- Computational
Molecular Biology
- This course is designed for molecular biologists and computer
scientists desiring a practical, hands on approach to the
field of computational molecular biology. The course is recommended
for those wanting to understand the major issues concerning
represe
- Computer
Intensive Methods in Phylogeny
- Computer
Intensive Methods in Phylogeny
- Stanford, Susan Holmes, Copyright 1998
- DEA-SIB:
Module 6
- Principles of Protein Structure, Comparative Protein Modelling
and Visualisation
- ETH:
Introduction to Bioinformatics
- The intention of this course is to provide biochemists
with a practical guide to bioinformatics. This will
be achieved by examining various software tools currently
available to the community. Our focus will lie both
on how one uses these tools and on
- Introduction
to the Bootstrap:Statistics 208
- Stanford, Susan Holmes, Copyright 1998
- IRBM
practical course
- Frontiers of Protein Structure Prediction 1995.
- Links2Go:
Bioinformatics: Academic/Degree Programs
- Not
Found
- Bioinformatics and Computational Biology at George Mason
University
- Scientists
complete genetic milestone
- Mapping DNA for Newbies from MSNBC
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