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ACeKit@elegansNet:  MATERIAL
C. elegans


  • Cell Analysis & Modeling Provides software tools for modeling cell physiological processes. Presented as Java applets, the tools are free to academic users (The National Resource for Cell Analysis and Modeling, NRCAM).
    • calcium waves sweeping across a neuron
    • mitochondrial respiration
    • nuclear envelope disintegration
Flow Cytometry
GFP & Bioluminescence
Oligoribonucleotides (Xeragon)

Software Collections: 


   C. elegans

    Collaboratory Tools:

  • Structural Biology

    • BioCoRE (Theoratical Biophysics Group, Urbana, Illinois, USA).


    Gene-finding software

  • ACEMBLY - A graphic interactive program to support shotgun and directed sequencing projects (Danielle & Jean Thierry-Mieg and Ulrich Sauvage, CNRS-CRBM, Montpellier, France).



  • EMBOSS suite of applications - a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community (read more in CCP11 News, 8/11/00). Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered:

    • Sequence alignment
    • Rapid database searching with sequence patterns
    • Protein motif identification, including domain analysis
    • EST analysis
    • Nucleotide sequence pattern analysis, for example to identify CpG islands.
    • Simple and species-specific repeat identification
    • Codon usage analysis for small genomes
    • Rapid identification of sequence patterns in large scale sequence sets.
    • Presentation tools for publication
    • And much more.
  • Fgenes+




  • GeneMarkHMM


  • GlimmerM

  • GeneBuilder

  • Genemark (The Borodovsky Group 
    School of Biology, 
    Georgia Institute of Technology).

  • HMMGene

  • MORGAN - an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier (S. Salzberg, A. Delcher, K. Fasman, and J. Henderson.  A Decision Tree System for Finding Genes in DNA).

  • SIM4 - addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors (Florea et al. 1998, Genome Res. 1998 8:967-74).

  • VEIL - the Viterbi Exon-Intron Locator uses a custom- designed hidden Markov model (HMM) to find genes in eukaryotic DNA (John Henderson, Steven Salzberg, and Ken Fasman at Johns Hopkins University).

  • Wise2/Genewise

    Gene Annotation-related 

         sites + Format & Tools

    Model Organisms 

         Projects & Databases

    Gnutella - a software tool 

        that can bypass Internet 

        service providers and 

        allow computer users to 

        communicate directly 

        among themselves.

   Statistical Analysis 

        access to many stat sites 

        offering online analysis 

        and tutorials (John C. 


  • Statistical Applets - provides basic online stat analysis (McGraw Hill - Vadum Rankin).

  • Sample Comparisons: t-Tests, ANOVAs, Non-parametric Comparisons (John C. Pezzullo).

  • StatSoft - covers basic statistics, experimental design, linear regression, and much more (HMS Beagle 4/12/00).

  •  StatView - Commercial site for downloading demo and purchasing StatView.

  • VassarStats - basic statistical number- crunching & procedure (Richard Lowry; Vassar College, NY,  USA) (Science review 5.26.00:"Lowry strives to demystify the "magic rituals" behind the process."


  • NAMD - a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems; distributed free of charge and includes source code (Theoretical Biophysics Group, Beckman Institute, U. Illinois, USA).

  • Protein Explorer - a RasMol-like interface implemented in Chime offering greater assistance and automation; visual exploration of protein structure & protein:DNA interactions are made easier & more convenient than RasMol; Need Netscape 4 or later. (Claude Aflalo, Ben Gurion U.; Beer Sheva,Israel; BNS June 2000).

  • VMD - a freely available Visual Molecular Dynamics program that currently runs on both windows and Unix (Theoretical Biophysics Group, Beckman Institute, U. Illinois, USA).

  • Webmolecules - View your favorite molecule form db of 21,000  (Molecular Arts Corp.).

  • WebMol - display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB); run as an applet or as a stand- alone application (Dirk Walther).

Vendors & Specialty       


   Buy sell used lab equip.

   Read lab product reviews

    Specialty Items   



Since 9/2/00; [last modified on 04/20/2003 ]  
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