Cn User: Peter Li

254?size=160x160

Name: Peter Li

Joined: Tuesday 13 November 2007 17:42:19 (UTC)

Last seen: Tuesday 20 May 2014 13:06:42 (UTC)

Email (public): Not specified

Website: Not specified

Location: Hong Kong, China

Peter Li has been credited 140 times

Peter Li has an average rating of:

4.5 / 5

(2 ratings in total)

for their items

Still enjoys eating at buffet restaurants. Currently, sampling the cuisine that Hong Kong has to offer. Need to be careful and watch my weight though.


Other contact details:

Not specified

Interests:

Systems biology, cheminformatics.

Field/Industry: Government agency

Occupation/Role(s): Data Organization Manager

Organisation(s):

BGI-Hong Kong

 

Note: some items may not be visible to you, due to viewing permissions.


Contents (click to expand/contract)
Uploader

Workflow Visualize PAV provenance as SVG (1)

Thumb
VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2014-05-20

Credits: User Peter Li

Uploader

Workflow Gene enhancer region analysis (1)

Thumb
 This Galaxy pipeline searches for transciption factor binding sites which are conserved through to Fugu. It then finds genes associated with these enhancer binding sites. See http://screencast.g2.bx.psu.edu/MAF_manipulation for the screencast that describes how this workflow is developed.

Created: 2012-06-14 | Last updated: 2012-07-06

Uploader

Workflow Advanced FastQ manipulation (1)

Thumb
 This Galaxy workflow performs advanced FastQ manipulation as demonstrated by the screencast at http://screencast.g2.bx.psu.edu/quickie_14_fastq_adv/flow.html. Given a FastQ set of data, it will be transformed using the tools, Groomer, Filter FastQ, FastQ Trimmer, Manipulate FastQ before it is finally converted into FASTA format.

Created: 2012-06-14 | Last updated: 2012-06-14

Uploader

Workflow Perform QC on FastQ data (1)

Thumb
 This Galaxy pipeline performs quality control analyses on FastQ data. A report is generated which provides various measures of the quality of the sequence reads.

Created: 2012-06-14 | Last updated: 2012-06-14

Uploader

Workflow galaxy_101 (2)

Thumb
  This is a Galaxy pipeline written using the Galaxy 101 tutorial (https://main.g2.bx.psu.edu/galaxy101). The pipeline involves retrieving genome and SNP data from UCSC for a particular chromosome. These data are integrated in order to find exons with the highest number of SNPs.

Created: 2012-06-13 | Last updated: 2012-06-14

Credits: User Peter Li

Uploader

Workflow Quality control processing of GEO datasets (2)

Thumb
The workflow performs a quality control process on gene expression data sets stored in the Gene Expression Omnibus database. The QC process is performed using Bioconductor R packages. A variety of statistics are produced by the workflow including a diagnostic plot from snm normalisation and nucleotide composition bias.

Created: 2011-04-06 | Last updated: 2011-04-11

Credits: User Peter Li User Bhmecham

Uploader

Workflow BioXSD example workflow (1)

Thumb
An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) Bioinformatics 26:i540-6. The workflow only calls one BioXSD web service (BLAST) since the second service (ClustalW) in the example workflow is currently down :(

Created: 2010-10-12 | Last updated: 2010-10-12

Credits: User Peter Li

Uploader

Workflow Generate CombiUgi library (1)

Thumb
Generates a CombiUgi library using data from a Goolgle spreadsheet containing smiles strings of compounds to undergo virtual Ugi reactions

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: User Peter Li User Romney

Uploader

Workflow Predict Abraham descriptors (1)

Thumb
Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values. The workflow returns all the Abraham descriptors E, S, A, B and V in a HTML file.Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values

Created: 2010-08-05 | Last updated: 2010-08-05

Credits: User Peter Li

Uploader

Workflow Predict chemical solubility in solvents (2)

Thumb
Predicts solubility in molar units for a given chemical compound represented as a SMILES string in a given solvent. Uses a beanshell script to enable the user to select the solvent from a list.

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: User Peter Li

Uploader

Workflow download (2)

Thumb
Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: User Peter Li

Uploader

Workflow PubChem substructure search (2)

Thumb
Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Uploader

Workflow smiles-identity-idlist (2)

Thumb
Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Uploader

Workflow smiles-identity-idlist (1)

Thumb
Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: User Peter Li

Uploader

Workflow file-similarity-entrez-url (2)

Thumb
Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: User Peter Li

Uploader

Workflow Simple search (1)

Thumb
Performs a lite search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Search structures in ChEBI database (1)

Thumb
 Does a substructure, similarity or identity search using a structure in the Chebi database

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get ontology children (1)

Thumb
Retrieves the ontology children of an entity including the relationship type, using the ChEBI identifier.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get ontology parents (1)

Thumb
Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get complete entity by list (1)

Thumb
Returns information from the chebi database for a list of chebi identifiers

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get complete chebi entity (1)

Thumb
Returns informations for a given compound represented by its chebi identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Asynchronous chemspider search by formula (1)

Thumb
Performs an asynchronous search on ChemSpider by molecular formula

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow getLiteEntity (1)

Thumb
Retrieves a list of "lite" entities containing only the ChEBI ASCII name and ChEBI identifier. The input parameters are a search string and a search category. If the search category is null then it will search under all fields. The search string accepts the wildcard character "*" and also unicode characters. You can get maximum results upto 5000 entries at a time.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow chemspider identifier to MOL format (1)

Thumb
Returns the MOL file for a given compound represented by its chemspider identifier

Created: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get structure synonyms (1)

Thumb
Returns synonyms for a given compound represented by a MOL fileReturns synonyms for a given compound

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get compound thumbnail (1)

Thumb
Returns a small image of the 2D structure of given chemical compound represented by its chemspider identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get compound information (1)

Thumb
Returns information about a given compound represented by its chemspider id

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Asynchronous chemspider simple search (1)

Thumb
Performs an asynchronous simple search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get spectrum information (1)

Thumb
Returns information about a spectrum identified by its chemspider spectrum identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get compound spectra information (1)

Thumb
Returns information about spectra stored in ChemSpider for a given compound represented by its chemspider identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get spectra information (1)

Thumb
Returns information about the spectra stored in ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: User Peter Li

Uploader

Workflow Get ChemSpider record in MOL format (1)

Thumb
Returns ChemSpider record in MOL format or empty string in case of failure.

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: User Peter Li

Uploader

Workflow Get extended compound information for a li... (1)

Thumb
 Returns information for a given list of chemspider compound identifiers.

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: User Peter Li

Uploader

Workflow Get extended compound information (1)

Thumb
Returns information from chemspider for a given chemical represented by its chemspider identifier

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: User Peter Li

Uploader

Workflow Get list of chemspider databases (1)

Thumb
Returns a list of databases catalogedReturns a list of databases cataloged by ChemSpider

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: User Peter Li

Uploader

Workflow Convert chemical identifier (1)

Thumb
Converts a chemical compound identifier from one format to another using the open babel web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow SmilesToInchi (1)

Thumb
Convert SMILES to InChI. Result is v1.02s InChI.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow MolToInchiKey (1)

Thumb
Converts a MOL file to an InChIKey. Result is v1.02s InChIKey.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow MolToInchiString (1)

Thumb
Converts a MOL file to InChI. Result is v1.02s InChI.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow isValidInChiKey (1)

Thumb
Checks that specified argument is valid InChIKey. Works for v1.02b InChIKey only.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InchiStringToSmiles (1)

Thumb
Converts an inchi string into SMILES format

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InChIStringToMolFile (1)

Thumb
Converts an InChI string into a MOL file using the Inchi ChemSpider web service

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InChIStringToInChiKey (1)

Thumb
Converts an InChI string to an InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InChIToCSID (1)

Thumb
Convert InChI to ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InChi key to MOL file (1)

Thumb
Returns a MOL file for a given InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InChi key to Inchi string (1)

Thumb
Converts an InChI key to an InChI string using the ChemSpider Inchi web service.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow InChi key to ChemSpider identifier (1)

Thumb
Returns Converts an InChIKey to a ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow Generate InChi key (1)

Thumb
Generates an inchi key for a given compound using the inchi web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow Generate inChi information (1)

Thumb
Uses the GenerateInchiInfo web service operation from ChemSpider to generate information relating to the InChi string for a given chemical compound

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow Generate inChi (1)

Thumb
Generates an inChi string for a given chemical represented by its SMILES string, SDF or MOL file using the inchi web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li

Uploader

Workflow AlitoraKDAInputModule test workflow (1)

Thumb
 This workflow calls the AlitoraKDAInputModule service from the test GenePattern server.

Created: 2010-07-07 | Last updated: 2010-07-07

Credits: User Peter Li

Uploader

Workflow Select items from list (1)

Thumb
This workflow pops up a window containing an input list of strings. The user is invited to select one or more strings for downstream processing.

Created: 2010-03-30

Credits: User Peter Li

Uploader

Workflow Copasi time simulation of SBML model (1)

Thumb
Uses the synchronous Copasi time simulation web service to predict the concentrations of species over a time period. The results from Copasi are provided in SBRML format which is visualised as a graph using an R script.

Created: 2010-03-26

Credits: User Peter Li

Uploader

Workflow SBML model optimisation (1)

Thumb
This workflow modifies reaction kinetic parameters against experimental data stored in the MCISB key results database

Created: 2010-03-26

Credits: User Peter Li

Uploader

Workflow SBML model parameterisation (1)

Thumb
This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow

Created: 2010-03-26

Credits: User Peter Li

Uploader

Workflow Construction of skeleton SBML model using ... (1)

Thumb
This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term.

Created: 2010-03-26 | Last updated: 2010-03-26

Credits: User Peter Li

Uploader

Workflow Construction of skeleton SBML model using ... (1)

Thumb
This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers

Created: 2010-03-26 | Last updated: 2010-03-26

Credits: User Peter Li

Uploader

Workflow Sage bionetwork demo workflow (1)

Thumb
This workflow performs key driver analysis and displays the results in Cytoscape.

Created: 2010-03-22

Credits: User Peter Li

Uploader

Workflow Invocation of Gene Pattern modules using R (1)

Thumb
 A workflow to invoke a Gene Pattern module using an R script. Note that a FTP URL for the data to be analysed is required, not the data itself!

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: User Peter Li

Uploader

Workflow Visualise KDA output data with Cytoscape (2)

Thumb
This workflow retrieves a data file on a web server directory and launches Cytoscape to visualise it.

Created: 2010-03-18 | Last updated: 2010-03-18

Credits: User Peter Li

Uploader

Workflow Test workflow for logging into Alitora and... (1)

Thumb
No description

Created: 2010-03-17

Credits: User Peter Li

Uploader

Workflow Log out from Alitora system (1)

Thumb
A nested workflow to be used for logging out of Alitora

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: User Peter Li

Uploader

Workflow Log into Alitora system (1)

Thumb
A nested workflow to be used for logging into Alitora

Created: 2010-03-17

Credits: User Peter Li

Uploader

Workflow Calculating frequencies of gene expression... (1)

Thumb
This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: User Peter Li

Uploader

Workflow Identification of differential genes using... (1)

Thumb
This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

Created: 2008-07-02 | Last updated: 2008-07-02

Credits: User Peter Li

Uploader

Workflow Identification of differential genes using... (2)

Thumb
This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

Created: 2008-04-15 | Last updated: 2008-07-01

Credits: User Peter Li

Uploader

Workflow selectworker (1)

Thumb
This workflow shows how the selectData beanshell script can be used to select items from a given list for analysis by downstream processors. Use Control and left mouse click to select multiple items.

Created: 2008-03-25 | Last updated: 2008-03-25

Credits: User Peter Li

Uploader

Workflow Mapping microarray data onto metabolic pat... (1)

Thumb
This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: User Peter Li

Uploader

Workflow Query Maxd microarray database (1)

Thumb
Retrieves data from the maxd database given name of data set

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: User Peter Li

What is this?

Linked Data

Non-Information Resource URI:


Alternative Formats

HTML
RDF
XML