User: Carol Lushbough

Name: Carol Lushbough

Joined: Thursday 23 October 2008 @ 15:43:02 (GMT)

Last seen: Monday 30 April 2012 @ 13:41:37 (GMT)

Email (public): clushbou [at] usd.edu

Website: http://bioextract.org

Location: Vermillion, SD, United States

1 Friend

1 Group (admin)

2 Groups (member)

6 Workflows

1 Packs

1 Files

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Carol Lushbough has been credited 7 times

Carol Lushbough has an average rating of:

4.0 / 5

(1 rating in total)

for their items

Carol Lushbough is an Assistant Professor of Computer Science at the University of South Dakota.
Her primary teaching areas include Systems Analysis, Software Engineering, and Bioinformatics.
In addition to her teaching responsibilities, she collaborates with Dr. Volker Brendel from
Iowa State University on the NSF funded project "Cyberinfrastructuer for (Comparative) Plant Genome
Research through PlangGDB". Her main contributes to the project is the development of the
BioExtract Server (http://bioextract.org). The BioExtract Server is a Web-based data integration
application designed to consolidate, analyze, and serve data from heterogeneous biomolecular
databases in the form of a mash-up. The basic operations of the BioExtract Server allow researchers,
via their Web browsers, to: specify data sources, flexibly query data sources, apply analytic tools,
download result sets, and store query results for later reuse. As a researcher works with the system,
their “steps” are saved in the background. At any time these steps can be preserved long-term as a
workflow simply by providing a workflow name and description.

Other contact details:

University of South Dakota

Interests:

Bioinformatics
Data Integration
Scientific Workflows

Field/Industry: Computer Science

Occupation/Role(s): Assistant Professor of Computer Science

Organisation(s):

University of South Dakota

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BioExtract Server Original Uploader Carol Lushbough	tblastx non-redundant alignment (v1) Created: 30/06/11 @ 15:26:13 \| Last updated: 04/07/11 @ 16:51:41 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species. For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1. Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2. The output from ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 4 times Tags (7): alignment \| gene \| genomic \| proteins \| sequence \| species \| workflow	View Download (v1)
BioExtract Server Original Uploader Carol Lushbough	Sequence Format Conversion (v1) Created: 28/06/11 @ 20:52:07 \| Last updated: 28/06/11 @ 21:03:58 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License Demonstrate the use of the format conversion tool. Converts a DNA sequence in fasta format into plain, genbank, and phylip formats. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 2 times Tags (1): conversion	View Download (v1)
BioExtract Server Original Uploader Carol Lushbough	Multiple Protein Alignment Profiling(1) (v4) Created: 13/01/10 @ 18:52:45 \| Last updated: 17/11/10 @ 14:13:20 Credits: Carol Lushbough Alan Williams Attributions: A workflow version of the EMBOSS tutorial License: Creative Commons Attribution-Share Alike 3.0 Unported License Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 152 times \| Downloaded: 60 times Tags (7): alignment \| ebi \| emma \| genomics \| prettyplot \| profile \| tmap	View Download (v4)
BioExtract Server Original Uploader Carol Lushbough	Phylogeny Bootstrapped Algorithm (v2) Created: 13/01/10 @ 18:47:06 \| Last updated: 17/11/10 @ 13:57:19 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License Bootstrapped sequences algorithm reads in a data set, and produces multiple data sets from it by bootstrap resampling. http://pro.genomics.purdue.edu/cgi-bin/emboss/help/fseqboot Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 204 times \| Downloaded: 130 times Tags (5): bioextract \| bootstrapp \| nucleotide \| phylogenetic tree \| phylogeny	View Download (v2)
BioExtract Server Original Uploader Carol Lushbough	Liliopsida Protein Alignment (v6) Created: 13/01/10 @ 18:42:35 \| Last updated: 17/11/10 @ 13:46:04 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow retrieves Liliopsida chloroplast petb gene sequences from NCBI Nucleotide, removes duplicate sequences and saves the results at BioExtract Server. These results are then converted into GenBank format and fed into Fetch Translation, which removes the translation from the CDS coding region. Translations are then used to build a multiple alignment using ClustalW. Rating: 4.0 / 5 (1 rating) \| Versions: 6 \| Reviews: 0 \| Comments: 3 \| Citations: 1 Viewed: 544 times \| Downloaded: 106 times Tags (5): alignment \| bioextract \| multiple sequence alignment \| nucleotide \| sequence alignment	View Download (v6)
BioExtract Server Original Uploader Carol Lushbough	Nucleotide InterProScan for the BioExtract Server (v3) Created: 16/04/09 @ 15:26:57 \| Last updated: 01/07/09 @ 08:32:34 Credits: Carol Lushbough Hamish McWilliam Attributions: Nucleotide_InterProScan License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 149 times \| Downloaded: 89 times Tags (5): bioinformatics \| BLAST \| blastp \| ebi \| interproscan	View Download (v3)