Wonder!

SILAC :: Stable isotope labeling with amino acids in cell culture

2007-01-12T17:02:00.000-05:00

SILAC :: Stable isotope labeling with amino acids in cell culture

Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometric (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given ‘‘light’’ or ‘‘heavy’’ form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, ¹³C, ¹⁵N). Thus in an experiment, two cell populations are grown in culture media that are identical except that one of them contains a ‘light’ and the other a ‘heavy’ form of a particular amino acid (e.g. ¹²C and ¹³C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%.

The site is developed and maintained by Pandey Lab.

HPRD: Human Protein Reference Database

2007-01-04T15:25:00.000-05:00

Human Protein Reference Database (http://www.hprd.org) is a web resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. Information that are cataloged were derived manually by critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.

Cited from http://en.wikipedia.org/wiki/HPRD

Tree of Life Web Project

2006-12-20T18:06:00.000-05:00

Tree of Life Web Project is a collaborative effort of biologists from around the world. On more than 5000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics.

Each page contains information about a particular group of organisms (e.g., echinoderms, tyrannosaurs, phlox flowers, cephalopods, club fungi, or the salamanderfish of Western Australia). ToL pages are linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.

A chapter on Patterson Function

2006-12-12T18:06:00.000-05:00

The Patterson Function

Eclipse Plug-In for R: "StatET"

2006-12-08T18:12:00.000-05:00

"StatET" is a small Eclipse plug-in, supporting you to write R scripts and documentations.

R is "a language and environment for statistical computing and graphics". Eclipse is "a kind of universal tool platform - an open extensible IDE for anything and nothing in particular". Both are available for many operation systems and can be used for free, and -of course- this plug-in too.

Population Education

2006-11-13T16:15:00.000-05:00

Population Education:

Get a Free USA at 300 Million Wall Chart

"2006 marks an historic milestone for our nation -- 300 million people. Over the past century, the population has tripled, making the United States the fastest growing developed country in the world, and the third largest overall. Reaching this marker offers an opportunity to reflect on our past, examine current trends and articulate our hopes for the future of American society."

The Jax Lab - Mice Genetics

2006-11-07T17:33:00.000-05:00

The Jackson Laboratory- Advancing Research in Human Health

They maintain over 3 ooo mouse strains, which are widely used around the world. Their website also hold a lot of FREE research resources on mouse genetics. Check it out at http://www.jax.org/

Answers.com - Online Dictionary, Encyclopedia and much more

2006-11-04T15:43:00.000-05:00

Answers.com - Online Dictionary, Encyclopedia and much more:

Embryo Images Online

2006-11-03T13:21:00.000-05:00

Embryo Images Online: Normal & Abnormal Mammalian Development

Olympus Microscopy Resource Center

2006-11-01T12:08:00.000-05:00

Olympus Microscopy Resource Center is designed to provide an Internet-based educational forum on all aspects of optical microscopy, photomicrography, and digital imaging. Many renowned manuals and interactive tutorials are avaible for FREE.
Also see Introduction to Optical Microscopy, Digital Imaging, and Photomicrography.

The WWW Virtual Library

2006-10-21T13:19:00.000-04:00

The WWW Virtual Library is the oldest catalogue of the Web, started by Tim Berners-Lee, the creator of HTML and of the Web itself, in 1991 at CERN in Geneva. Unlike commercial catalogues, it is run by a loose confederation of volunteers, who compile pages of key links for particular areas in which they are expert; even though it isn't the biggest index of the Web, the VL pages are widely recognised as being amongst the highest-quality guides to particular sections of the Web.

Agriculture
Irrigation, Livestock, Poultry Science, …
The Arts
Art History, Classical Music, Theatre and Drama, …
Business and Economics
Finance, Marketing, Transportation, …
Communications and Media
Broadcasters, Publishers, Telecommunications, …
Computing and Computer Science
Artificial Intelligence, Cryptography, Logic Programming, …
Education
Primary, Secondary, Tertiary, …
Engineering
Architecture, Electrical, Mechanical, …
Humanities and Humanistic Studies
History, Languages and Linguistics, Museums, …

Information and Libraries
Information Quality, Knowledge Management, Libraries, …
International Affairs
International Relations and Security, Sustainable Development, …
Law
Arbitration, Forensic Toxicology, Legal History, …
Natural Sciences and Mathematics
Biosciences, Earth Science, Medicine and Health, Physics, …
Recreation
Gardening, Recreation and Games, Sport, …
Regional Studies
African, Asian, Latin American, European, …
Social and Behavioural Sciences
Anthropology, Archaeology, Population and Development Studies, …
Society
Peoples, Religion, Gender Studies, …

The World-Wide Web Virtual Library: Statistics

2006-10-17T21:03:00.000-04:00

The World-Wide Web Virtual Library: Statistics

The World Wide Web Virtual Library: Statistics

This page is being brought to you by the folks at The University of Florida's Department of Statistics.
The "book and globe" logo is the trademark of the WWW Virtual Library.

Data Sources

Statistical Reference Datasets (StRD)

Job Announcements

The Job Announcements are maintained at UF. Announcements may be sent via email to jobs@stat.ufl.edu .

Departments, Divisions, and Schools of Statistics

Listings by Continent: [Africa] [Asia] [Australia/Oceania] [Europe] [North America] [South America]

On-Line Educational Resources

Government Statistical Institutes

Statistical Research Groups, Institutes, and Associations

Statistical Services

Advanced Quantitative Services
BS Statistics
Business Statistics (Graduate)
Stat-Ease
Stat Guide Online
Statistical Data Analysis (Undergraduate)
Systems Simulation (Graduate)
Venturi Technology Partners

Statistical Archives and Resources

A Bare Bones Introductory Statistics Text Book
Bibliography for Computational Probability and Statistics
Bibliography for Discrete Event Simulation
Bibliography for Optimization with Sensitivity Analysis
CHANCE Database
CSIRO QStats Software a directory of statistical software sites
David Dowe's Mixture Modelling Page
Fortran 90 Web Site of Alan J. Miller -- Fortran code for statistics
Free Statistical Tools on the Web
JASA Data Archive
GAMS: Guide to Available Mathematical Software
Introductory Statistics: Concepts, Models, and Applications
Macintosh-based statistics software
Math Jobs -- Listing of Jobs Related to Mathematics
Netlib (Mathematical and Statistical Software)
Probability/Statistics Object Library
PASE
Quick-Start Guide to Common Calculators
Manuscript Collections in the Statistical Archive, Iowa State University Library
Service Industries Trends (SItrends.org)
StatLib Index
Statistics HomePage -- Electonic Statistics Texbook
Statistics on the Web
StatsNet
stats.repsys.net
SunSITE, Austria -- Computer Support for Mathematics, Statistics & Science Education
Tutorials: Statistics
U.S. Bureau of Labor Statistics
U.S. Census Bureau

Statistical Software Vendors and Software FAQs

Accumetric Corporation -- AccuCon, AccuROC
Analyse-It Software Ltd. -- Analyse-It for Microsoft Excel
Analytical Software -- Statistix
Aptech Systems -- GAUSS
Automatic Forecasting Systems -- AUTOBOX
Circle Systems -- Stat/Transfer
Click and Learn Regression
CoHort Software -- Graphics and Statistics Software for Scientists and Engineers
Creascience -- XLSTAT
CyTEL Software Corporation -- StatXact, LogXact, EaSt
Data Description, Inc. -- Data Desk, Viz!on, ActivStats
Data Step -- Free SPSS tutorial and statistical selection guide
Data Shaping Solutions
DOS-based statistics software
DTREG -- Generates classification and regression decision trees.
ESB Consultancy -- ESBStats, ESBPDF, ESBCalc
Exeter Software -- NTSYSpc
Expert Health Data Programming -- Vitalnet
GRABITECH
GraphPad Software -- Prism, InStat
High Performance Systems -- ithink, STELLA
InterLeap
John Galt Solutions -- ForecastX
Kovach Computing Services -- xlSTAT, MVSP
Leading Market Technologies -- EXPO
Lumina Decision Systems -- Analytica
Macsyma Inc. -- Macsyma, PDEase2D
Manugistics, Inc. -- STATGRAPHICS
Mathsoft, Inc. -- Mathcad and S-PLUS
MATHSTATICA Pty Ltd - mathStatica
Mathtools.com -- Complementary products for MATLAB
Mathtools.net -- Portal for MATLAB
MathWorks -- MATLAB
MedCalc
MicroMetrix -- AssiStat
Mike McLaughlin -- Regress+ for MacOS
Minitab, Inc.
MultiSimplex
NCSS
NLREG -- Performs general nonlinear regression.
Numerical Algorithms Group -- Genstat, GLIM, NAG Libraries
OriginLab -- Origin
Partek Pro Software
POSDEM -- Software to choose between sampling plans
Process Builder -- STRATEGY
ProGAMMA -- Software for the Social and Behavioral Sciences
Provalis Research -- SIMSTAT
QQQ Software -- TPL Tables
Qualitran's Statistical Software
Resampling Stats
Raynald's SPSS Tools, Archive, Tips, FAQ and Tutorials
Salford Systems - Statistical Software and Consulting
The SAS Institute
Obtaining SAS Notes through Email
Scolari Sage Publications -- GB STAT
Seventh Sense Software -- Chameleon Statistics
S-Matrix Corporation -- CARD - Design Of Experiments software for Windows
SPSS
Scientific Software International -- LISREL & HLM
The S FAQ
SmallWaters Corp.Amos structural equation modeling
Stata Corporation
Stat-Ease
Statistical Solutions -- SOLAS for Missing Data Analysis
Statpoint.com -- STATGRAPHICS Plus, STATLETS, STATBEANS
StatSoft, Inc. -- STATISTICA
StatsDirect
Statit Software -- Statit e-QC, Statit e-Server, Statit Custom QC
StudySize
SUDAAN
Visual Numerics Inc. -- PV-Wave, IMSL, Stanford Graphics.
Wolfram Research -- Mathematica
xlSTAT HomePage
XLStatistics
XploRe -- Interactive Statistical Computing Environment
XTREMES

Statistical Journals

Mailing Lists and Archives

AI-Geostats, a Geostatistics mailing list
Allstat
Allstat Web Intro
Genstat (searchable archive)
List of Statistics Lists
S-news
SAS-L (WAIS Archive)
SPSS-L (WAIS Archive)

Statistics Related News Groups

Related Fields

From: http://www.stat.ufl.edu/vlib/

3DGenome Project

2006-10-05T22:33:00.000-04:00

3DGenome Project consortium members will develop state-of-the-art 3D light microscopy techniques, along with image processing and analysis tools to visualise DNA inside the cell. They will correlate the genome's 3D structure with the expression of specific genes in human, mice and drosophila cells. Using this range of model systems will help establish which aspects of the 3D genome structure have been conserved through evolution and which are most likely to play an important role in gene regulation.

The research program is conducted by a consortium of seven European partners and is coordinated by Roel van Driel of the Swammerdam Institute for Life Sciences of the University of Amsterdam in The Netherlands.

The EU Sixth Framework Programme (FP6) for Research and Development (2002-2006) is one of the world's largest research programmes, with a budget of 17.5 billion Euros, of which around 3 billion Euros is available for life sciences research. Under the FP6, 2.2 million Euros have been awarded to the 3DGENOME-research program.

Molecular Probes - The Handbook - A Guide to Fluorescent Probes and Labeling Technologies(10th)

2006-10-05T15:49:00.000-04:00

The Handbook — A Guide to Fluorescent Probes and Labeling Technologies is a comprehensive resource for fluorescence technology and its applications. Newly revised, The Handbook contains detailed information describing the use of more than 3000 Molecular Probes products for life science research, including extensive data, numerous technical notes, and full-color images of the products in action.

Introduction to Fluorescence Techniques

Chapter 1
Fluorophores and Their Amine-Reactive Derivatives

Chapter 2
Thiol-Reactive Probes

Chapter 3
Reagents for Modifying Groups Other Than Thiols or Amines

Chapter 4
Biotin Derivatives and Haptens

Chapter 5
Crosslinking and Photoactivatable Reagents

Chapter 6
Ultrasensitive Detection Technology

Chapter 7
Antibodies, Avidins, Lectins and Related Products

Chapter 8
Nucleic Acid Detection and Genomics Technology

Chapter 9
Protein Detection and Proteomics Technology

Chapter 10
Enzyme Substrates

Chapter 11
Probes for Cytoskeletal Proteins

Chapter 12
Probes for Organelles

Chapter 13
Probes for Lipids and Membranes

-

Chapter 14
Fluorescent Tracers of Cell Morphology and Fluid Flow

Chapter 15
Assays for Cell Viability, Proliferation and Function

Chapter 16
Probes for Endocytosis, Receptors and Ion Channels

Chapter 17
Probes for Signal Transduction

Chapter 18
Probes for Reactive Oxygen Species, Including Nitric Oxide

Chapter 19
Indicators for Ca{2+}, Mg{2+}, Zn{2+} and Other Metal Ions

Chapter 20
pH Indicators

Chapter 21
Indicators for Na{+}, K{+}, Cl{-} and Miscellaneous Ions

Chapter 22
Probes for Membrane Potential

Chapter 23
Tools for Fluorescence Applications, Including Reference Standards and Optical Filters

Technical Notes and Product Highlights

List of Tables

List of Figures

Provided by

GeneScape Portal

2006-10-05T10:46:00.000-04:00

GeneScape® is CuraGen's state-of-the-art operating portal that provides the foundation for genomic-based drug discovery and development. GeneScape is a sophisticated bioinformatics platform that was developed at CuraGen to manage, track, analyze, and interpret industrial scale genomic information. The GeneScape operating portal integrates each of CuraGen's functional genomic technologies and enables access via the Internet.

Gene Ontology Tools

2006-10-02T00:19:00.000-04:00

Gene Ontology Tools

Tools for searching and browsing GO

Annotation tools

Tools for gene expression/microarray analysis

Other tools

Consortium Tools

The tools below are developed within the Gene Ontology Consortium. They continue to be improved and expanded and you can receive support in using these tools by writing to the GO helpdesk.

The tools on this page are free to academics.

AmiGO

Berkeley Bioinformatics and Ontology Project
No abstract available

AmiGO allows you to search for a GO term and view all gene products annotated to it, or search for a gene product and view all its associations. You can also browse the ontologies to view relationships between terms as well as the number of gene products annotated to a given term. AmiGO accesses the GO mySQL database; the browser and documentation are available from the GO database website.

AmiGO is developed and maintained within the GO Consortium.

OBO-Edit

Berkeley Bioinformatics and Ontology Project
No abstract available

OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies.
OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.
OBO-Edit was previously known as DAG-Edit.
OBO-Edit uses the OBO format flat file.
OBO-Edit is developed and maintained within the GO Consortium.

Non-Consortium Tools

Many tools have been created outside of the consortium for use with the GO ontologies. To see listings of these tools please use the links in the table below.

Tools for searching and browsing GO

Tool to display, browse and search the ontologies and/or annotations.

Annotation tools

Tools for annotating genes or gene products using GO

Tools for gene expression/microarray analysis

Other tools

Submit new tools

How to request that your tool be listed on these pages.

From: http://www.geneontology.org/GO.tools.shtml

Data Analysis BriefBook

2006-09-25T15:56:00.000-04:00

The Data Analysis BriefBook is a condensed handbook, or an extended glossary, written in encyclopedic format, covering subjects in statistics, computing, analysis, and related fields. It intends to be both introduction and reference for data analysts, scientists and engineers.

Moved to Wonder! China

2006-06-26T17:20:00.000-04:00

Friends in China can not visit Blogger, so I finally decide to move to Wonder！- Learning .:&:. Amusement (http://sparkw.mysmth.net/) or visit by another address given by China's SciBlogger Association (http://biowonder.sciblogs.org）

Please visit my home page http://jieqi.info for other sharing.

Gene Ontology

2006-06-15T23:19:00.000-04:00

Gene Ontology(GO) project is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes. The three organizing principles of GO are molecular function, biological process and cellular component.

General Repository for Interaction Datasets

2006-06-15T23:16:00.000-04:00

General Repository for Interaction Datasets (GRID) is a comprehensive database of Genetic and Physical Interactions in several organisms, including yeast, fly and worm. They also develop a software named Osprey to view those interactions locally. Osprey builds data-rich graphical representations from Gene Ontology(GO) annotated interaction data maintained by The GRID.

Directory of Grants and Fellowships in the Global Health Sciences

2006-06-15T13:13:00.000-04:00

The Fogarty International Center, the international component of the National Institutes of Health, addresses global health issues through research and training programs and participates in international partnerships to foster research and improve health. Since 1988, the Center has published the Directory of International Grants and Fellowships in the Health Sciences, a comprehensive compilation of international funding opportunities in biomedical and behavioral research. RSS Feed.

Phobius

2006-06-15T13:10:00.000-04:00

Phobius: "A combined transmembrane topology and signal peptide predictor"

Eukaryotic Promoter Database (SIB)

2006-06-15T02:05:00.000-04:00

SIB-EPD is an annotated non-redundant collection of eukaryotic POL II promoters. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Powered by Swiss Institute for Bioinformatics

Saccharomyces Genome Database

2006-06-14T12:41:00.000-04:00

SGD^TM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

Bioinformatics: Sequence and Genome Analysis (2nd Edt)

2006-06-14T02:02:00.000-04:00

Read it Online
The second edition of Bioinformatics: Sequence and Genome Analysis provides comprehensive instruction in computational methods for analyzing DNA, RNA, and protein data, with explanations of the underlying algorithms, the advantages and limitations of each method, and strategies for their application to biological problems.

Common Links for Biologist

2006-06-12T03:13:00.000-04:00

Amos'WWW links page :ExPASy Life Science Directory
NCBI: National Center for Biotechnology Information
ExPASy: Expert Protein Analysis System Proteomics Server
PDB: Protein Data Bank

Journals: (Imapact Factor 2004)
Cell; Nature; Science; PLoS (Public Library of Science)

ExPASy Proteomics Server

2006-06-12T03:09:00.000-04:00

ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE (Disclaimer / References), includingSwiss-Prot and TrEMBL ,PROSITE ,SWISS-2DPAGE ,ENZYME and many Proteomics and sequence analysis tools

Visual Complexity

2006-06-09T18:25:00.000-04:00

VisualComplexity.com intends to be a unified resource space for anyone interested in the visualization of complex networks. The project's main goal is to leverage a critical understanding of different visualization methods, across a series of disciplines, as diverse as Biology, Social Networks or the World Wide Web.

Nature | Milestones

2006-06-08T10:20:00.000-04:00

Nature Milestones highlights key discoveries that have shaped different scientific fields and enables the wider recognition of these classic findings that are often recognized only by those in the field.

From

Scansite

2006-06-08T10:19:00.000-04:00

Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains. The current release version 2.0 includes 62 motifs characterizing the binding and/or substrate specificities of many families of Ser/Thr- or Tyr-kinases, SH2, SH3, PDZ, 14-3-3 and PTB domains, together with signature motifs for PtdIns(3,4,5)P(3)-specific PH domains
See reference.

Cytoscape: Analyzing and Visualizing Biological Network Data

2006-06-08T10:09:00.000-04:00

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. The platform supports gene functional annotations from Gene Ontology (GO) and KEGG databases, biological models from Systems Biology Markup Language (SBML), protein-protein interactions from BIND and TRANSFAC databases. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. See features and tutorial. More information about the Cytoscape platform and project is available on the Web at www.cytoscape.org.

Recommended plugins:
Agilent Literature Search

Institute for Systems Biology
University of California at San Diego

Memorial Sloan-Kettering Cancer Center
Agilent Technologies

Institut Pasteur

PhosphoSite

2006-06-07T12:48:00.000-04:00

PhosphoSite is a curated bioinformatics database developed by scientists at Cell Signaling Technology. Its goal are to aggregate information about all in vivo phosphorylation sites in human and mouse proteins and to provide information and resources that will facilitate signal transduction research. It now contains selected literature references, the peptide sequences of phosphorylation sites, their location within known domains and motifs, links to useful resources, and sources of antibodies for studying these sites.

Science | Special Issues

2006-06-06T21:31:00.000-04:00

Science| Online Extras: Special Issues provide an archive of Science's Special Issues, as well as Special Issue-related collections of articles drawing on material from both the journal and its online companion sites. A comprehensive site for special topic!

Science's STKE | Connections Map

2006-06-06T21:24:00.000-04:00

Science's STKE | Connections Map provide a graphical interface to a database of information on components of cellular signaling pathways and their relations. Pathway Authorities recruited by the editorial staff of the STKE provide the information in the database.

Address change and related problems

2006-06-06T13:20:00.000-04:00

I noticed one the problem related to the blog address change.
The JCR (Journal citation report) should be found here.

Declaration about blog addresses

2006-06-01T21:53:00.000-04:00

Blog Wonder! has changed the address to http://biowonder.blogspot.com, which is maintained by spark,Zhang,qqkk and Abhijit.
The current address of http://sparkw.blogspot.com has NO relationship with spark. And Wonder! CN (http://sparkw.mysmth.net) is the sister blog of Wonder! in China, which is maintained both by sparkw@newsmth and biowonder@newsmth.
Both of these blogs are initiated to provide colleagues with biology-related web resources.

A Biotechnology Science Primer | NCBI

2006-05-25T15:31:00.000-04:00

A Biotechnology Science Primer - Education resources at NCBI:
Bioinformatics, Genome Mapping, Molecular Modeling, SNPs, ESTs, Microarray Technology, Molecular Genetics, Pharmacogenomics Phylogentics.

Podcasts in Science

2006-05-24T21:48:00.000-04:00

Nature Podcast
http://www.nature.com/nature/podcast/rss/nature.xml

Science & the City | New York Academy of Sciences
http://www.nyas.org/podcasts/nyaspodcast.xml

Subscribe podcasts with a media player, such as iTunes from Apple.

New Harrison's series

2006-05-24T20:52:00.000-04:00

McGraw Hill recently launched its new medical professional site, Harrison's Practice. The sister Text, Harrison's Principle of Internal Medicine, is world known medicine book for its up-to-date medical info. This new practice site focuses more on clinical aspect, while Principle targets more on underneath mechanism.

DNA Microarray

2006-05-24T13:09:00.000-04:00

DNA Microarray

Microarrays: Chipping Away at the Mysteries of Science and Medicine, a Science Primer from the National Center for Biotechnology Information (NCBI).

Educator Resources from Affymetrix, a manufacturer of microarrays. Includes, among many other things, photographs, a description of Affymetrix's unique manufacturing method, and a discussion of ethics and policy issues. You can even order your own free demonstration microarray!

Photo of a microarray manufactured by Agilent Technologies
Fluorescent image of a microarray manufactured by Agilent Technologies
Find out how DNA microarray analysis is being used to study insecticide resistance in African malaria-carrying mosquitoes.

Science & the City | New York Academy of Sciences

2006-05-22T23:41:00.000-04:00

Science & the City New York Academy of Sciences delivers a podcast featuring interviews, conversations, and lectures by noted scientists and authors. You can subscribe to our podcast feed so that our latest audio presentations are brought to your desktop, or you can preview individual presentations. In addition, you can access journalist reports with video, resource links, and more, at www.nyas.org.

Science Functional Genomics Resources: Gene Expression

2006-05-21T20:13:00.000-04:00

Gene Expression: Pointers to selected online resources on gene expression and microarrays.

Microarray Gene Expression Data Society

2006-05-21T16:59:00.000-04:00

Microarray Gene Expression Data Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.

ImageJ

2006-05-20T19:29:00.000-04:00

ImageJ:Image Processing and Analysis in Java. Free and available for many platforms.

《数字创世纪——人工生命的新科学》

2006-05-11T00:39:00.000-04:00

《数字创世纪——人工生命的新科学》
作者：李建会张江
“人工生命，是一个充满着深刻的思想、有趣的模型和丰富的隐喻的新领域。然而让人遗憾的是该领域的中文图书实在少之又少。于是，我们便萌生了写作这本书的想法。……然而计算机中的涌现模型恰恰是该领域思想方法的主要内核，如果不了解其中的细节很难把握住它的主流。所以，本书非常强调具体计算机模型的说明和讨论。”
（点击直接阅读）

Artificial Neural Networks Technology

2006-05-09T20:58:00.000-04:00

A book on Artificial Neural Networks Technology. Prepared by Dave Anderson and George McNeil.

Read online or download the postscipt file at here

Commonly Used Force Fields

2006-05-09T00:41:00.000-04:00

MM2, MM3 and MM4(N. L. Allingeret al.)
small organic molecules
http://europa.chem.uga.edu/index.html
MMFF(Merck Molecular Force Field, proposed by T. A. Halgren)
biomolecules
T.A. Halgren, J. Comput. Chem. 17, 490 (1996)
AMBER(Assisted Model Building with Energy Refinement, by P. A.
Kollmanet al.)
biomolecules
http://www.amber.ucsf.edu/amber/amber.html
Optimized Potentials for Liquid Simulation, W. L. Jorgensen et al)
organic liquids
W. Damm, A. Frontera, J. Tirado-Rives, W.L. Jorgensen, J. Comput.Chem. 18, 1955 (1997);
CHARMM(Chemistry at HARvardMacromolecular Mechanics, by M.Karplusand coworkers)
biomolecules
http://www.charmm.org/
ECEPP(Empirical Conformational Energy Program for Peptides, by H. A. Scheragaet al.)
biomolecules
http://www.tc.cornell.edu/Research/Biomed/CompBiologyTools/eceppak/
http://www.chem.cornell.edu/has5/
GROMOS(GROningenMOlecularSimulation, by W. F. van Gunsterenand coworkers)
biomolecules
http://www.igc.ethz.ch/gromos/

Loop Database

2006-05-08T13:55:00.000-04:00

Wloop database: Profiles encode using HCA matrix + ending point distance restrictions
http://bioserv.rpbs.jussieu.fr/cgi-bin/WLoop
Sloop classification: Profiles encoded using FUGUE matrices; only sequence
http://www-cryst.bioc.cam.ac.uk/~sloop
ArchDB classification: Profiles encoded using HMM models; only sequence
http://sbi.imim.es/archdb
Loops in Proteins database:
http://www.protein-design.com/LIP/

new NAS members

2006-05-03T23:49:00.000-04:00

2006 new elected full LIST

Members in NYC
FUTUYMA, Douglas J.; Distinguished Professor of Ecology and Evolution, department of ecology and evolution, State University of New York, Stony Brook

GILBERT, Charles D.; professor, Laboratory of Neurobiology, Rockefeller University, New York City

GOFF, Stephen P.; investigator, Howard Hughes Medical Institute, and professor of biochemistry and molecular biophysics, department of biochemistry and molecular biophysics, Columbia University College of Physicians and Surgeons, New York City

GREENGARD, Leslie; professor of mathematics and computer science, Courant Institute, New York University, New York City

McDERMOTT, Ann E.; professor of chemistry, department of chemistry, Columbia University, New York City

NOVICK, Richard P.; investigator, Skirball Institute for Biomolecular Medicine, and professor of medicine and microbiology, New York University School of Medicine, New York City

O'DONNELL, Michael E.; investigator, Howard Hughes Medical Institute, and professor, Laboratory of DNA Replication, Rockefeller University, New York City

RAVETCH, Jeffrey V.; Theresa and Eugene M. Lang Professor, and head, Laboratory of Genetics and Immunology, Rockefeller University, New York City

吉林大学Elmo站－数学

2006-04-29T18:46:00.000-04:00

吉林大学Elmo站:

数学相关书籍、软件等

用户登陆后三十分钟内允许可免费下载五个个文件，如需要继续请在三十分钟后再来下载

Stem cell News site

2006-04-28T20:16:00.000-04:00

As you may know and my blog featured, California initiatives for stem cell got ok from the court, while the plantiff was planning to appeal.

I found this news through latest Science mag, while yahoo search gave MedicalNNewsToday news site. Even better, the MedicalNNewsToday also has a section for the hot stem cell research. Wish you enjoy it as I do.

Books on Complexity

2006-04-24T20:48:00.000-04:00

How Nature Works: The Science of Self-Organized Criticality
by Per Bak
Ubiquity : Why Catastrophes Happen
by Mark Buchanan
Complexity: The Emerging Science at the Edge of Order and Chaos
by Mitchell M. Waldrop
Chaos: Making a New Science
by James Gleick
Sync: The Emerging Science of Spontaneous Order
by Steven Strogatz
Also called "How Order Emerges from Chaos in the Universe, Nature, and Daily Life"
Foundations of Complex-system Theories : In Economics, Evolutionary Biology, and Statistical Physics
by Sunny Y. Auyang

Swiss EMBnet node server

2006-04-23T11:33:00.000-04:00

Swiss EMBnet node server provides services including:

Basic BLAST Sequence searches
Advanced BLAST Sequence searches
TMPRED Transmembrane regions detection
LALIGN Alignments of 2 sequences
PRSS Optimal score of an alignment
COILS Coiled-coil domains prediction
BOXSHADE Multiple alignments designer
ClustalW Multiple sequence alignment
T-COFFEE Multiple sequence alignment
iPCR Virtual PCR tool
EMBOSS/wEMBOSS package
ENSEMBL local mirror site
SRS7 searches at EBI
Fetch get sequences

FTP server Databases and software download

Phylogeny Programs

2006-04-20T21:28:00.000-04:00

Developers of Phylip collect hundreds of links and descriptions of Phylogeny Programs in the world.

EMBL Dali: 3-D protein structure superposition

2006-04-20T01:53:00.000-04:00

EMBL Dal server compares protein structures in 3D against those in the Protein Data Bank. If you want to know the structural neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database.

Medical Dictionary

2006-04-19T20:59:00.000-04:00

As a health care professional, good medical dictionary is a must! I have used several dictionaries, and found Intellihealth was the very best. I continue using it...

The site is www.intellihealth.com Under "Look it up" menu. Of note, online www.webster.com is another good one for general use.

Pattern Search

2006-04-19T01:52:00.000-04:00

PROSITE: single motifs (regexs) -best with small highly conserved sites
eMOTIF: permissive regexs(derived from PRINTS and BLOCKS)
Profile Library: weight matrices-good with divergent domains and superfamilies
PRINTS: multiple motifs (fingerprints) -best for families and sub-families
Blocks: multiple motifs (derived from InterPro and PRINTS)
Pfam: Hidden Markov Models -good with divergent domains and superfamilies

InterProScan

2006-04-19T01:37:00.000-04:00

InterProScan: Searching of many motif databasesat the same time.

BlastProDom	FPrintScan	HMMPIR	HMMPfam	HMMSmart
HMMTigr	ProfileScan	ScanRegExp	SuperFamily	SignalPHMM
TMHMM	HMMPanther	Gene3D

Evolutionary Trace Servers

2006-04-19T01:27:00.000-04:00

ET method maps clusters of subfamily specific residues on 3D structures. See here for an overview.
Severs:
@University of Cambridge(with support from PHYLIP)
@Baylor College of Medicine

Amas - Analyze Multiply Aligned Sequences

2006-04-18T21:42:00.000-04:00

Amas: "is a program to analyse multiple alignments of protein sequences. It allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree, and generates pretty coloured alignments". Download it for free or do analyze on the web server.

orkut community

2006-04-12T22:15:00.000-04:00

is an online community that connects people through a network of trusted friends.

It provides the network and friend list function, by which one can quickly expand his network/community. Also a forum funtion makes it very easy to set up a place where people can easily share their values and comments, maybe critics.

I made a community of CMG (Chinese medical graduates), for the benefit of Chinese medical graduates, who are struglling for USMLE, and residency match.

Free Vector NTI Software

2006-04-11T22:47:00.000-04:00

Vector NTI Advance™ - Sequence analysis and data management software. It provides full-featured, highly integrated desktop bioinformatics applications. Invitrogen launches the Vector NTI Open Access Policy.Now non-profit researchers can get FREE, annual licenses of Vector NTI software in 3 Easy Steps. View the full policy here.

Special Topics

2006-04-11T16:24:00.000-04:00

ESI Special Topics is designed to complement Essential Science Indicators in providing citation analyses and commentary for selected scientific research areas that have experienced notable recent advances or are of special current interest.

Drosophila Resources

2006-03-31T18:07:00.000-05:00

Berkeley Drosophila Genome Project: http://www.fruitfly.org
Flybase: http://flybase.net/

For moe links on fruit fly, see here

Good site for translation

2006-03-29T13:00:00.000-05:00

I'd like to suggest a good dictionary site for online translation, dict.cn.

It's the one maintained by IU students. Personally, I like it very much for its simplicity and broad coverage. Of note, most of the words were marked with American English pronunciation.

Retrieval of awarded grants

2006-03-27T18:25:00.000-05:00

Computer Retrieval of Information on Scientific Projects: A Database of Biomedical Research Funded By the National Institutes of Health (NIH). It includes projects funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Health Care Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH).

Good website for health info

2006-03-26T15:02:00.000-05:00

Here, I strongly recommend a good site for general public, www.familydoctor.org.

The site was made by American Academy of Family Medicine, and covers common diseases. I found the tools part was very useful. They compiled a algorithm in symptom part of Tools.

MITOP project

2006-03-21T16:44:00.000-05:00

Mitochondrial Proteome Project is to provide a comprehensive list of mitochondrial proteins of yeast and man. Datasets relevant to the study of the mitochondrial proteome are integrated and accessible via search tools and links. They include computational predictions of signalling sequences and summarize results from proteome mapping, mutant screening, expression profiling, protein-protein interaction and cellular sublocalisation studies. old version

PSORT WWW Server

2006-03-21T16:31:00.000-05:00

PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information." Mirrors at Tokyo, Okazaki, and Peking

HapMap Homepage

2006-03-16T10:37:00.000-05:00

HapMap is a catalog of common genetic variants that occur in human beings. It describes what these variants are, where they occur in our DNA, and how they are distributed among people within populations and among populations in different parts of the world. It is designed to provide information that other researchers can use to link genetic variants to the risk for specific illnesses, which will lead to new methods of preventing, diagnosing, and treating disease. See here for the origin of haplotype.

The match day for residency

2006-03-13T11:11:00.000-05:00

Today, every American and internatinal medical graduate starts to know if they are lucky enough to get a slot in the Match of residency for this year, or have to struggle in the post match Scramble, where one has another, if not the last, chance of entering residency program in 2006.

Good luck to all!

Physical Review Online Archive

2006-03-09T17:06:00.000-05:00

PROLA Homepage hosts the archives for Phys. Rev. A-E, ST AB, ST PER, Lett., Focus; Rev. Mod. Phys. and so on.

Cancer stem cells

2006-03-08T10:29:00.000-05:00

Cancer stem cells are a new and old concept. It's been proposed decades ago, and recently has drawn many attentions with progress in developmental biology and stem cells, including embryonic and somatic.

A recent review/perspective on cancer stem cells was published in Nat Med 12, 296 - 300 (2006)

BioPerl

2006-03-07T22:24:00.000-05:00

BioPerl: Perl for bioinformatics. Bioperl project's community documentation site.

Database Categories @ Nucleic Acids Research

2006-03-07T21:31:00.000-05:00

Database Summary Paper Categories maitained by Nucleic Acids Research

History of Delevopmental Genetics III

2006-03-03T12:14:00.000-05:00

History of Delevopmental Genetics III: Scott F. Gillbert reviewed the induction and the orgins of developmental genetics. It focused on the work of Salome Gluecksohn-Schoenheimer (later S. Gluecksohn-Waelsch; 1907 - ) (left) and Conrad Hal Waddington (1905 - 1975)(right), including the concept of canalization from Waddington

Networks / Pajek

2006-03-03T11:41:00.000-05:00

Pajek is for large network analysis. It runs on Windows and nicely runs on Linux via Wine. Free for noncommercial use.

Measurement Unit Converter

2006-03-02T09:44:00.000-05:00

Measurement Unit Converter
Click here for specific conversions between China & America

International Conference on Systems Biology - 2005

2006-02-27T14:41:00.000-05:00

Most of the presentations on ICSB 2005 Conference are now available online.

California stem cell agency fights for life

2006-02-27T12:30:00.000-05:00

It was a great news the Proposition 71 was backed by 59% of electorate. The proposition 71 authorized the agency, California Institute of Regenerative Medicine, to dole out an average of $300 million in research grants each year over 10 years. However, at least a couple of lawsuits are seeking to invalidate the creation of CIRM, which put the institute in trouble. Several scientists have to turn down Stanford offer, due to lack of funding that was supposed to come after the foudation of CIRM, but has not yet. From Yahoo SciNews.

Sad for the stem cell scientists.

Wikipedia

2006-02-25T23:07:00.000-05:00

Wikipedia: The free encyclopedia that anyone can edit", and the project is described as "an effort to create and distribute a multilingual free encyclopedia of the highest possible quality to every single person on the planet in their own language."

Scale-free Network

2006-02-24T13:48:00.000-05:00

In scale-free network, the very few network nodes (called "hubs") were far more connected than other nodes. The probability that a node connects with k other nodes was proportional to k^−γ, where γ is between 2 and 3. Many real networks fall in this group, such as Word Wide Web (Internet), protein-protein interaction, sexual partners in humans, social network and so on.
Barabási A.L. et al. wrote an review, named Scale-free networks, on Scientific American in 2003. Here is a general introduction on Wipipedia.

Hot microbiology! -Change your major now?

2006-02-24T11:19:00.000-05:00

Current issue of Cell is a collection of hot topics in microbiology. Several interesting reviews focus on viruses, bacteria, and immunity. Apparently, it becomes easier to find a job with micro PhD than others. NIH fundings for micro were also increased though others were flattened-corret me if I am wrong.

Ten worst presentation habbits

2006-02-23T09:49:00.000-05:00

Presentation skills are an essential not only for business elites, but also for biomedical researchers. Here BW (Businessweek) recently represented a good list of bad habbits. So check you own way of speaking in front of audience!

I cite the list brieftly,

reading from notes
avoiding eye contacts
dressing down
diggling, fidgeting, and swaying
failure to rehearsal
standing at attention
speaking too long
fail to excite
end with an inspiration deficit

The Linux Documentation Project

2006-02-22T17:45:00.000-05:00

The Linux Documentation Project: "TLDP is short for The Linux Documentation Project, an organization of volunteers authoring, reviewing and managing documents about the Linux operating system. Documents basically come in two formats HOWTOs and guides."

First contribution

2006-02-22T16:36:00.000-05:00

I was delighted to join this group, and wish it would become a useful resource for biomedical researchers.

Finding a job is a big headache for student, postdoc, even for junior faculty. Here I recommend naturejobs. Many pieces of good advice, prospective, and profiles of working area were featured. I do enjoy every issue of it, and hope you like it as I do.

Internet FAQ Archives - Online Education

2006-02-22T16:08:00.000-05:00

Internet FAQ Archives - Online Education: "This archive contains Usenet Frequently Asked Questions (FAQ) postings in HTML format and in text format."

Emacs Tiny Tools Project

2006-02-22T15:11:00.000-05:00

Emacs Tiny Tools Project homepage: "Tiny Tools is an on-going 'hobby', that started with one Emacs package, then next, and next in 1994 to help use Emacs more conveniently in daily work."

Faculty of 1000 Biology

2006-02-17T17:39:00.000-05:00

Faculty of 1000 Biology is a new online research tool that highlights the most interesting papers in biology, based on the recommendations of over 1000 leading scientists.

The R Project for Statistical Computing

2006-02-17T17:33:00.000-05:00

R is a language and environment for statistical computing and graphics. It is similar to the S language and environment. It's a GNU project.

GSL - GNU Scientific Library

2006-02-07T19:44:00.000-05:00

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total. It is free software under the GNU General Public License.

TNT Home Page

2006-01-11T17:41:00.000-05:00

TNT is a collection of interfaces and reference implementations of numerical objects useful for scientific computing in C++. The toolkit defines interfaces for basic data structures, such as multidimensional arrays and sparse matrices, commonly used in numerical applications.

MathWorld

2006-01-09T13:44:00.000-05:00

MathWorld is assembled over more than a decade by internet encyclopedist Eric W. Weisstein with assistance from the mathematics and internet communities. It quotes itself as the web's most extensive mathematics resource.

Overview of Cot analysis - Daniel G. Peterson

2005-11-29T13:26:00.000-05:00

Roy Britten and his colleagues designed in the 1960s

Nucleic Acid Database (NDB)

2005-11-29T11:05:00.000-05:00

a repository of three-dimensional structural information about nucleic acids

Functional Genomics Resources: Epigenetics

2005-11-28T20:48:00.000-05:00

From Science Magazine

RasMol and OpenRasMol

2005-11-02T23:12:00.000-05:00

RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and and software developers of open source versions of RasMol.

RasMol Home Page

2005-10-31T23:17:00.000-05:00

Protein Explorer, a RasMol-derivative, is the easiest-to-use and most powerful software for looking at macromolecular structure and its relation to function. And it's free! It runs on Windows or Macintosh/PPC /Linux/Unix computers.RasMol users will find its menus very familiar, and it understands RasMol commands. It is very fast: rotating a protein or DNA molecule shows its 3D structure"

Science--Enhanced Perspectives and Policy Forums Listing

2005-10-27T00:53:00.000-04:00

Science's Enhanced Perspectives are concise overviews of exciting recent research, either published in Science or elsewhere. Enhanced Perspectives include hypernotes beyond the standard bibliographic references. Once a month, they also provide an enhanced version of a Science Policy Forum article.

On Being the Right Size

2005-10-19T23:30:00.000-04:00

On Being the Right Size is a 1928 essay by J.B.S. Haldane. It discusses proportions in the animal world and the essential link between the size of an animal and these systems an animal has for life.