 |
|
|
|
Bio-Informatics Tools / Software
Licensed and locally developed software available at the Leiden Genome Technology Center
Other software recommended by the LGTC
- Sanger Sequencing, view and/or align traces
- Applied Biosystems Sequence Scanner
- Codon Code
- Staden Package
Licensed software available at the LGTC
Program: Rosetta Resolver
Functions: The CMSB-NBIC Rosetta Resolver system is a multi-user system for the storage and analysis of gene expression microarray data
Introduction: Website, Dr. Peter Taschner
Program: Axon GenePix 6.0
Functions: Image analysis and quality report of spotted microarrays
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Introduction: Website
Program: Agilent Feature extraction software
Functions: Image analysis of Agilent microarrays
Where: Agilent scanner computer, room R04-021
No Data storage: do not store data on the Agilent scanner PC, at some point it will be deleted
Program: NimbleScan
Functions: Image analysis of NimbleGen microarrays
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Login: Ask LGTC to be authorized to access the NimbleScan PC
Introduction: Website
Program: Ingenuity Pathway Analysis active from November 4th, 2008 until November 4th, 2010
Functions: Search and explore molecules (genes, drugs, etc.), build pathways, overlay gene expression on pathways, search for pathways with gene expression data, search for tissue-specific gene expression, etc. for human, mouse and rat.
Where: Web-based
Introduction: Weekly web trainings from Ingenuity Systems; additional questions can be addressed to Judith Boer or the LGTC.
Login: Contact the LGTC for log-in information
IPA user rules: Please be aware that by logging in, you are aware of and agree with the following:
- The Ingenuity Pathway Analysis license is active until November 4, 2009. In case the license is not extended you will not have access to your analyses after that date. Export of lists and images is possible.
- You should save your analyses, pathways, etc. ONLY in a folder Name_Project under My Projects. Results that are saved in different places may be deleted.
- All IPA users in the Center for Human and Clinical Genetics have access to all data stored in the LGTC account.
- You will be informed of weekly training sessions (Thursdays 16:00 our time) and scientific seminars by Ingenuity Systems.
- You should direct your questions for IPA customer support to Judith Boer, Sophie Greve or the LGTC.
- Do not forward the login and password information to new users. Tell them to mail the LGTC. We would like to keep track of the users with registration via us.
Program: Spotfire Decision Site for Functional Genomics
Functions: Analysis and visualization of microarray and chip data, including data filtering, normalization, hierarchical clustering, k-means clustering, profile search, classification
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Login: ask LGTC for ID and password
Introduction: Web-guides
Program: MaRe: Microarray Retriever
Functions: This tool enables batch retrieval of microarray data matching your search criteria
Where: Web based
Program: CORE_TF
Functions: Identifying Conserved and Over-Represented Transcription Factors
Where: Web based
Program: Affymetrix total desktop mining solution
Functions: absolute and comparison analysis of Affymetrix chip files, storage of maximum of 100 chips in a personal database, datamining including data filtering, t-test, and self-organizing maps
Where: Free to download from Affymetrix website
Introduction: Web-guides
Program: Illumina GenomeStudio for Illumina microarrays
Functions: analysis and visualization of microarray and chip data, including data filtering, normalization, hierarchical clustering, k-means clustering, profile search, classification
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Login: Ask LGTC to be authorized to access the GenomeStudio PC
Introduction: Handbook, web-guides
Program: Softgenetics Mutation Surveyor
Functions: rapid location of all differences between the wild type sequence and sample traces
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Introduction:Web-guides
Program: Applied Biosystems Gene Mapper
Functions: sizing and pattern recognition for any fragment analysis
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Login: ask LGTC for ID and password
Introduction: Web-guides
Program: Softgenetics Gene Marker
Functions: sizing and pattern recognition for any fragment analysis
Where: Network license available via the LGTC
Introduction: Web-guides
Program: Illumina GenomeStudio for Illumina Next Gen Sequencing
Functions: Analyze primary sequence-based Genome Analyzer data
Where: LGTC PC available in room R5-24
Reservation: agenda (mandatory) in room R5-24
Registration: registration list (mandatory) in room R5-24
No Data storage: do not store data on the LGTC PC, at some point it will be deleted
Login: Ask LGTC to be authorized to access the GenomeStudio PC
Introduction: Web-guides
Information
Contact the LGTC.
|
|
