Site Outline for Nomi's obligatory home page (http://www.fruitfly.org/~nomi/)

Depth: 3; Children: 20

0. Nomi Harris: Biography

0.0. http://www.fruitfly.org/~nomi/nomi-images/nh-santa-fe.jpg
0.1. Princeton University *
0.2. MIT LCS Clinical Decision Making Group *
0.3. Massachusetts Institute of Technology *
0.4. NCBI HomePage *
0.5. The Cohen Lab *
0.6. 500 Can't connect to www.axyspharm.com:80 (Timeout) : (http://www.axyspharm.com/) *
0.7. 500 Can't connect to www.doubletwist.com:80 (Bad hostname 'www.doubletwist.com') : (http://www.doubletwist.com/) *
0.8. BDGP: Home
0.9. Lawrence Berkeley National Laboratory *
0.10. UC Berkeley home page *
0.11. BDGP: Genomic DNA Sequencing Project

0.11.0. BDGP: Home
0.11.1. BDGP: Home
0.11.2. BDGP: BDGP Information
0.11.3. BDGP: Searches
0.11.4. BDGP: Fly BLAST
0.11.5. BDGP: GadFly: Genome Annotation Database of Drosophila
0.11.6. FlyBase All Searches *
0.11.7. BDGP: Analysis Tools
0.11.8. BDGP: Genome Projects
0.11.9. BDGP: Genomic DNA Sequencing Project
0.11.10. BDGP: cDNA & EST Projects
URL redirected to http://www.fruitfly.org/EST/
0.11.11. BDGP: Transposon Insertions
0.11.12. BDGP: Single Nucleotide Polymorphism (SNP) Maps
0.11.13. BDGP: BDGP Resources
0.11.14. BDGP: Download BDGP Sequence and Annotation Databases
0.11.15. BDGP: Materials
0.11.16. BDGP: BDGP Publications
0.11.17. BDGP: Laboratory Methods
0.11.18. FlyBase @ flybase.bio.indiana.edu *
0.11.19. BDGP: Release 3 Notes
0.11.20. BDGP: ArmView: Chromosome Arm Map Viewer

0.12. About Genotator

0.12.0. Genotator: A Workbench for Sequence Annotation
0.12.1. What Genotator needs
0.12.2. Praise for Genotator
0.12.3. Genotator: A Workbench for Sequence Annotation
0.12.4. Genome Research *
0.12.5. Genotator licensing agreement
0.12.6. Nomi's obligatory home page
(see this outline for children)

0.13. Apollo Genome Annotation Tool

0.13.0. BDGP: Home
0.13.1. FlyBase @ flybase.bio.indiana.edu *
0.13.2. Ensembl Genome Browser *
0.13.3. BDGP: Release 3 Notes
0.13.4. Generic Model Organism Database Construction Set *
0.13.5. Install Apollo Genome Annotation Tool
0.13.6. Genome Biology | Full text | Apollo: a sequence annotation editor *
0.13.7. Genome Biology *
0.13.8. Apollo FAQ
0.13.9. Apollo User Guide
0.13.10. apollo Info Page *
0.13.11. SourceForge.net: Project Filelist *
0.13.12. Generic Model Organism Database Construction Set *
0.13.13. Open Source Initiative OSI - The Artistic License:Licensing *

0.14. BOSC 2002 *
0.15. 404 Not Found: (http://www.jax.org/courses/documents/tigr03.html) *
0.16. WAVE Women *
0.17. 404 Not Found: (http://www.rsn.com/snow/snowreport.html?state=CA) *
0.18. Jeremy Wilkinson Harris *
0.19. Tim Wilkinson *
0.20. Jeremy Wilkinson Harris *

1. Nomi Harris's List of Publications

1.0. Genome Biology | Full text | Apollo: a sequence annotation editor *
1.1. Genome Biology *
1.2. Genome Biology | Full text | An integrated computational pipeline and database to support whole-genome sequence annotation *
1.3. Genome Biology *
1.4. Genome Biology | Full text | Annotation of the Drosophila melanogaster euchromatic genome: a systematic review *
1.5. Genome Biology *
1.6. 500 Can't connect to 64.240.195.39:80 (Timeout) : (http://64.240.195.39/humana/FMPro?-db=humana%5fonline.fp3&-format=journaldetail.htm&-lay=journal%20description&-sortfield=catalog%3a%3aPub.%20Date&-sortorder=descend&Product%20Type=Journal&-op=cn&Keys=molecular%20biotechnology&-max=10&-recid=3&-token=12637279&-find=) *
URL redirected to http://64.240.195.39/humana/FMPro?-db=humana_online.fp3&-format=journaldetail.htm&-lay=journal%20description&-sortfield=catalog%3A%3APub.%20Date&-sortorder=descend&Product%20Type=Journal&-op=cn&Keys=molecular%20biotechnology&-max=10&-recid=3&-token=12637279&-find=
1.7. Project VirGO *
1.8. Genome Research -- Abstracts: Reese et al. 10 (4): 483 *
1.9. Genome Research *
1.10. http://www.genome.org/content/vol10/issue4/cover.gif *
1.11. http://www.fruitfly.org/GASP1/paper/Reeseetal/figs/Cover.jpg
1.12. Science -- Abstracts: Adams et al. 287 (5461): 2185 *
1.13. Science -- Abstracts: Rubin et al. 287 (5461): 2204 *
1.14. Pointer to Conference Page *
Redirected via META-tag to http://www.tigr.org/cet/gss/cg/index.shtml.
1.15. BDGP: Genome Annotation Assessment Project - GASP1

1.15.0. BDGP: Home
1.15.1. BDGP: Home
1.15.2. BDGP: BDGP Information
1.15.3. BDGP: Searches
1.15.4. BDGP: Fly BLAST
1.15.5. BDGP: GadFly: Genome Annotation Database of Drosophila
1.15.6. FlyBase All Searches *
1.15.7. BDGP: Analysis Tools
1.15.8. BDGP: Genome Projects
1.15.9. BDGP: Genomic DNA Sequencing Project
1.15.10. BDGP: cDNA & EST Projects
URL redirected to http://www.fruitfly.org/EST/
1.15.11. BDGP: Transposon Insertions
1.15.12. BDGP: Single Nucleotide Polymorphism (SNP) Maps
1.15.13. BDGP: BDGP Resources
1.15.14. BDGP: Download BDGP Sequence and Annotation Databases
1.15.15. BDGP: Materials
1.15.16. BDGP: BDGP Publications
1.15.17. BDGP: Laboratory Methods
1.15.18. FlyBase @ flybase.bio.indiana.edu *
1.15.19. Genome Annotation Experiment Description
1.15.20. Format for Submissions to Genome Annotation Experiment

1.16. 403 Forbidden: (http://ismb99.gmd.de/) *
1.17. 500 Can't connect to 204.30.25.100:80 (Timeout) : (http://204.30.25.100/humana/FMPro?-db=humana%5fonline.fp3&-format=detail.htm&-lay=book%20detail&-sortfield=catalog%3a%3aPub.%20Date&-sortorder=descend&catalog%3a%3aseries=Methods%20in%20Molecular%20Biology&-max=10&-recid=33256&-token=12599758&-find=) *
URL redirected to http://204.30.25.100/humana/FMPro?-db=humana_online.fp3&-format=detail.htm&-lay=book%20detail&-sortfield=catalog%3A%3APub.%20Date&-sortorder=descend&catalog%3A%3Aseries=Methods%20in%20Molecular%20Biology&-max=10&-recid=33256&-token=12599758&-find=
1.18. 404 Object Not Found: (http://www.humanapress.com/humana/FMPro?-db=humana_online.fp3&-format=default.htm&-lay=hitlist&-token=12599760&Product%20Type=Book&-sortfield=catalog%3A%3APub.%20Date&-sortOrder=descending&-max=10&-find=&-op=eq&catalog%3A%3ABestseller=Bestseller) *
1.19. http://www.fruitfly.org/publications/PDF/ADH.pdf
URL redirected to http://www.fruitfly.org/about/pubs/index.html
1.20. Computational Genomics Conference - The Institute for Genomic Research *

2. Apollo Genome Annotation Tool

2.0. BDGP: Home
2.1. FlyBase @ flybase.bio.indiana.edu *
2.2. Ensembl Genome Browser *
2.3. BDGP: Release 3 Notes

2.3.0. BDGP: Home
2.3.1. BDGP: Home
2.3.2. BDGP: BDGP Information
2.3.3. BDGP: Searches
2.3.4. BDGP: Fly BLAST
2.3.5. BDGP: GadFly: Genome Annotation Database of Drosophila
2.3.6. FlyBase All Searches *
2.3.7. BDGP: Analysis Tools
2.3.8. BDGP: Genome Projects
2.3.9. BDGP: Genomic DNA Sequencing Project
2.3.10. BDGP: cDNA & EST Projects
URL redirected to http://www.fruitfly.org/EST/
2.3.11. BDGP: Transposon Insertions
2.3.12. BDGP: Single Nucleotide Polymorphism (SNP) Maps
2.3.13. BDGP: BDGP Resources
2.3.14. BDGP: Download BDGP Sequence and Annotation Databases
2.3.15. BDGP: Materials
2.3.16. BDGP: BDGP Publications
2.3.17. BDGP: Laboratory Methods
2.3.18. FlyBase @ flybase.bio.indiana.edu *
2.3.19. Entrez-Nucleotide *
URL redirected to http://www.ncbi.nih.gov/entrez/query.fcgi?db=Nucleotide
2.3.20. Lawrence Berkeley National Laboratory *

2.4. Generic Model Organism Database Construction Set *
2.5. Install Apollo Genome Annotation Tool

2.5.0. Install Apollo Genome Annotation Tool
(Children already printed--see section 2.5)
2.5.1. InstallAnywhere and PowerUpdate by Zero G: Multi-platform software installation and updating *
URL redirected to http://www.zerog.com/
2.5.2. http://www.fruitfly.org/annot/apollo/InstData/Windows/VM/install.exe
2.5.3. http://www.fruitfly.org/annot/apollo/InstData/Windows/NoVM/install.exe
2.5.4. Install Apollo Genome Annotation Tool#windows
2.5.5. http://www.fruitfly.org/annot/apollo/InstData/MacOSX/install.zip
2.5.6. Install Apollo Genome Annotation Tool#macosx
2.5.7. http://www.fruitfly.org/annot/apollo/InstData/Solaris/VM/install.bin
2.5.8. Install Apollo Genome Annotation Tool#solaris
2.5.9. http://www.fruitfly.org/annot/apollo/InstData/Linux/VM/install.bin
2.5.10. http://www.fruitfly.org/annot/apollo/InstData/Linux/NoVM/install.bin
2.5.11. Install Apollo Genome Annotation Tool#linux
2.5.12. http://www.fruitfly.org/annot/apollo/InstData/GenericUnix/install.bin
2.5.13. Install Apollo Genome Annotation Tool#unix
2.5.14. StuffIt Expander: Unzip zip, access StuffIt files, free *
URL redirected to http://www.stuffit.com/expander/index.html
2.5.15. Java(TM) Platform Ports *
URL redirected to http://java.sun.com/cgi-bin/java-ports.cgi
2.5.16. Java(TM) Platform Ports *
URL redirected to http://java.sun.com/cgi-bin/java-ports.cgi
2.5.17. InstallAnywhere and PowerUpdate by Zero G: Multi-platform software installation and updating *
URL redirected to http://www.zerog.com/
2.5.18. InstallAnywhere and PowerUpdate by Zero G: Multi-platform software installation and updating *
URL redirected to http://www.zerog.com/
2.5.19. Apple *
2.5.20. Sun Microsystems *

2.6. Genome Biology | Full text | Apollo: a sequence annotation editor *
2.7. Genome Biology *
2.8. Apollo FAQ

2.8.0. Apollo User Guide
2.8.1. Install Apollo Genome Annotation Tool
(Children already printed--see section 2.5)
2.8.2. Install Apollo Genome Annotation Tool
(Children already printed--see section 2.5)
2.8.3. apollo Info Page *
2.8.4. http://www.fruitfly.org/annot/apollo/gamexml.dtd.txt
2.8.5. The Sanger Institute : GFF *
2.8.6. Distributed Annotation System *
2.8.7. Ensembl Genome Browser *
2.8.8. Apollo User Guide #configuration
2.8.9. SourceForge.net: Project Info - Generic Model Organism System Database *
URL redirected to http://sourceforge.net/projects/gmod/
2.8.10. Naked Mole Rat *
2.8.11. NCBI BLAST Home Page *
2.8.12. New GENSCAN Web Server at MIT *
2.8.13. http://www.fruitfly.org/annot/apollo/gamexml.dtd.txt
2.8.14. http://www.fruitfly.org/annot/apollo/example.xml
2.8.15. Ensembl Genome Browser *
2.8.16. Ensembl Genome Browser *
2.8.17. SourceForge.net: Submit New Issue/Request *
2.8.18. Install Apollo Genome Annotation Tool
(Children already printed--see section 2.5)

2.9. Apollo User Guide

2.9.0. Apollo User Guide #Introduction
2.9.1. Apollo User Guide #Community
2.9.2. Apollo User Guide #Bugs
2.9.3. Apollo User Guide #Mailing
2.9.4. Apollo User Guide #Download
2.9.5. Apollo User Guide #StartingUp
2.9.6. Apollo User Guide #StartingUnix
2.9.7. Apollo User Guide #StartingWindows
2.9.8. Apollo User Guide #FirstView
2.9.9. Apollo User Guide #stdout
2.9.10. Apollo User Guide #Loading
2.9.11. Apollo User Guide #ReadingXML
2.9.12. Apollo User Guide #ReadingGFF
2.9.13. Apollo User Guide #ReadingEnsembl
2.9.14. Apollo User Guide #Reading_Ensembl_via_ensj
2.9.15. Apollo User Guide #Styles
2.9.16. Apollo User Guide #DisplayPanels
2.9.17. Apollo User Guide #MainWindow
2.9.18. Apollo User Guide #AnnotationsVsResults
2.9.19. Apollo User Guide #Splitters
2.9.20. Apollo User Guide #Zooming

2.10. apollo Info Page *
2.11. SourceForge.net: Project Filelist *
2.12. Generic Model Organism Database Construction Set *
2.13. Open Source Initiative OSI - The Artistic License:Licensing *

3. Generic Model Organism Database Construction Set *
4. About Genotator
(Children already printed--see section 0.12)
5. Praise for Genotator

5.0. About Genotator
(Children already printed--see section 0.12)

6. OutaSite: A program to make site outlines

6.0. Site Outline for http://www-hgc.lbl.gov/homes/nomi/

6.0.0. http://www-hgc.lbl.gov/homes/nomi/ *
Redirected via META-tag to http://www.fruitfly.org/~nomi/.
6.0.1. http://www-hgc.lbl.gov/inf/annotation.html *
Redirected via META-tag to http://www.fruitfly.org/~nomi/genotator/.
6.0.2. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0
6.0.3. http://www-hgc.lbl.gov/homes/nomi/ *
Redirected via META-tag to http://www.fruitfly.org/~nomi/.
6.0.4. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0
6.0.5. 500 Can't connect to fruitfly.berkeley.edu:80 (Timeout) : (http://fruitfly.berkeley.edu) *
6.0.6. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0
6.0.7. 500 Can't connect to fruitfly.berkeley.edu:80 (Timeout) : (http://fruitfly.berkeley.edu/BDGP/informatics/bioTkperl.html) *
6.0.8. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0
6.0.9. 500 Can't connect to cbil.humgen.upenn.edu:80 (Bad hostname 'cbil.humgen.upenn.edu') : (http://cbil.humgen.upenn.edu/~dsearls/bioTk.html) *
6.0.10. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0
6.0.11. http://www-hgc.lbl.gov/projects/promoter.html *
Redirected via META-tag to http://www.fruitfly.org/seq_tools/promoter.html.
6.0.12. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0.4
6.0.13. Promoter prediction instructions *
6.0.14. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0.4.0
6.0.15. Abstract Improved Eukaryotic Promoter Site Recognition *
6.0.16. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0.4.0
6.0.17. 500 Can't connect to www.pharm.ucsf.edu:80 (Bad hostname 'www.pharm.ucsf.edu') : (http://www.pharm.ucsf.edu/psb/psb96/proceedings/eproceedings.html) *
6.0.18. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0.4.0
6.0.19. 500 Can't connect to cgl.ucsf.edu:80 (Timeout) : (http://cgl.ucsf.edu/psb/psb96) *
6.0.20. Site Outline for http://www-hgc.lbl.gov/homes/nomi/#0.4.0

6.1. Downloading OutaSite

6.1.0. GNU General Public License - GNU Project - Free Software Foundation (FSF) *
6.1.1. OutaSite: A program to make site outlines
6.1.2. Site Outline for http://www-hgc.lbl.gov/homes/nomi/
(Children already printed--see section 6.0)
6.1.3. Nomi's obligatory home page
(see this outline for children)
6.1.4. Nomi's obligatory home page
(see this outline for children)

6.2. Site Outline for http://www-hgc.lbl.gov/homes/nomi/
(Children already printed--see section 6.0)
6.3. Downloading OutaSite
(Children already printed--see section 6.1)
6.4. Nomi's obligatory home page
(see this outline for children)

7. WAVE Women *
8. Nomi & Tim's feline companion animals *
9. Jeremy Wilkinson Harris *

Depth: 3.
Maximum number of children explored from any parent: 20.

This page was created on Mon Apr 14 15:16:33 2003 by OutaSite version 2.0 (Time-stamp: <03/03/23 15:32:42 nomi>), written by Nomi Harris and Wim Rijnders.