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For Use by ICCB-L/NSRB Small Molecule and RNAi Screeners
Spotfire
Ingenuity Analysis Pathway
Scitegic Pipeline Pilot
GeneGo MetaCore
1. Spotfire Decision Site
Spotfire is an interactive data visualization tool that enables screeners to graph very large data sets for the purposes of identifying outlying data points (e.g. hits) and for comparing data sets. This software is only available on the analysis PC in SGM 604. You will need a Harvard Medical School eCommons name and password to log on to the computer.
After clicking on the Spotfire desktop icon, enter (both are case sensitive):
username - Screener
password - ICCBL
A 'Getting Started' box will open that provides an introduction to the software. You can open data files from your directory on an HMS file server, or from a CD or other portable memory device. More details on using Spotfire will be coming.
2. Ingenuity Pathways Analysis
Ingenuity is a biological pathway analysis tool that allows screeners to identify relationships among genes identified in RNAi screens.
You can sign into Ingenuity from any computer that has a Web connection. For information on using Ingenuity, click here to access the HMS Mammalian RNAi Wiki. You will need a Harvard Medical School eCommons username and password for access. For more information on getting access to the RNAi Wiki, click here.
For those who do not require RNAi wiki access, as of 8/1/09
ICCB-L/NSRB screeners now can create individual password protected IPA
accounts. With the new system any stored data files will not be
accessible to other users. This is available to screeners at HMS and
affiliated institutions (those with e-mail addresses with harvard.edu
or partners.org domains; other users please see instructions below). To
create a new account, go to http://www.ingenuity.com and click on the text "Add Me to My Institution's License" (upper right hand of page) and follow the instructions. Please contact David Wrobel (david_wrobel"AT"hms.harvard.edu) for the instituion license key. If you keep that field blank you will only be able to sign up for a 14 day trial. If you have had a free trial of IPA in the past, send your request to support@ingenuity.com and a notification will be sent when the account is created (usually within 1 business day).
Users at institutions that are not affiliated with HMS (i.e. if you do not have a harvard.edu or partners.org e-mail address) should contact David Wrobel for a general access user account and password. This will operate like the previous system, with any stored data visible to others using that account.
If you have data in one of the previous five shared accounts, you can have any stored data files moved to your private account by sending a request with the e-mail address account id you used and file names to support@ingenuity.com.
3. Scitegic Pipeline Pilot
Pipeline Pilot is very useful for analyzing screening data. It can rapidly analyze large datasets with user-specified computational protocols that are assembled in a modular fashion. Although the application's full functionality is available on only one workstation at the ICCB-L/NSRB screening facility (in SGM 604), protocols may be accessed anywhere with a web browser via the Pipeline Pilot Webport interface. A number of commonly requested analytical functions are provided (see list below), and additional ones will be made available as they are developed by screening facility staff. Webport users cannot write new protocols or modify existing ones, but the screening facilities staff can create custom protocols upon request. Webport is accessible only with an Internet Explorer browser using Windows. You will need to establish a HMS VPN (virtual private network) connection if outside the HMS network. Click here for login to "Secure Access SSL VPN" -- then click "Network Connect". For your first login you will be prompted to download software. An active eCommons ID and password are required for establishing VPN and login to Webport.
(contact katrina_rudnicki"AT"hms.harvard.edu if you need an ecommons ID)
Click here to access the SciTegic server for Webport (login as a Webport User to "Pipeline Pilot Webport").
Currently available protocols are listed in the "Protocols for Screeners" folder. Click on the desired protocol to show instructions, then click on the blue protocol name in the instructions field to load the protocol. Each protocol has fields for source and input files, and any user-changeable parameters. Protocol descriptions and output file formats are specified in the help section.
Available Webport protocols
- Calculate ALogP: Uses the atom-based method published by Ghose and Crippen to calculate the predicted octanol-water partition coefficient (LogP) and the molar refractivity (MR) for all compounds listed in an input Excel file based on plate and well coordinates.
- Calculate Molecular Weights: Calculates molecular weights for all compounds listed in an input Excel file based on plate and well coordinates.
- Cluster Molecules in an Excel File: Compounds from an Excel input file are partitioned into groups of structurally similar compounds (clusters) based on Tanimoto similarities.
- Cluster Molecules in an SD File: Compounds from an SD input file are partitioned into groups of structurally similar compounds (clusters) based on Tanimoto similarities.
- Collect Information from Compound Libraries: Collects compound structures and information from ICCB-Longwood/NSRB small molecule libraries and outputs one file using plate and well names from an input file as identifiers.
- Combine Excel Worksheets: Combines all Excel worksheets from one workbook to one worksheet.
- Filter Screen Result Positives: Filters all wells designated as positive in multiple annotated screen result files.
- Join Data Files: Using a data column common to two input files (the query file and file to match), outputs a file with all records that are present in both (based on the specified column or columns to match). A second output file includes all data in the file to be matched that did not match the query file.
- Lipinski Filter: Filters input SD file(s) based on Lipinski's Rule of Five.
- Molecular Weight Filter: Filters compounds from an input SD file based on the selected molecular weight range.
- Search Compound Libraries using SMILES Strings: Uses SMILES strings as input to search against the complete ICCB-Longwood/NSRB compound library database.
- SMILES Canonicalization: Converts an input list of SMILES strings to the canonical versions, which is useful when attempting to generate a standardized list. Canonical SMILES is a form of SMILES that is independent of how the molecule is drawn and can be used to compare whether two molecules are identical.
- Structure Similarity Filter: Starting with a specific single compound query structure entered as a SMILES string, identifies structurally similar compounds in the active and retired ICCB-Longwood/NSRB libraries database.
Pipeline Pilot: http://accelrys.com/products/scitegic/
VPN: https://secure.med.harvard.edu/dana-na/auth/url_default/welcome.cgi
SciTegic Server: http://pipeline-pilot.med.harvard.edu:9944/
4. GeneGo MetaCore
MetaCore (from GeneGo) is a software package for data mining and development of pathways and networks for genes and proteins of interest identified in RNAi screens.
This Web-based analysis tool is available for use by ICCBL/NSRB screeners at Harvard Medical School and affiliated institutions (if you have a Harvard e-mail address). To obtain your own account username and password, please contact David Osterbur (david_osterbur"AT"hms.harvard.edu) at HMS Countway Medical Library. MetaCore is available on Mac or PC, using Internet Explorer, FireFox or Safari.
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