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Blob Big Data paper supplementary material ZIP archive

Created: 2013-06-19 07:44:10

Credits: User pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Pack Big Data 2013 Paper Supplementary Material


Created: 2013-06-19 07:40:14 | Last updated: 2013-06-19 07:44:43

The zip file contains the datasets used for the evaluation of  our BigData paper "Pinar Alper, Khalid Belhajjame, Carole Goble, and Pinar Karagoz. Small is beautiful: Summarizing scientific workflows using semantic an- notations. In Proceedings of the IEEE 2nd International Congress on Big Data (BigData 2013), Santa Clara, CA, USA, June 2013."

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Taverna 2
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30?size=60x60 Nl Marco Roos

Workflow OPS_FreetextToTargetInfo (1)

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Workflow to retrieve target information for the concepts as refered to by humans (the input). Known issues: It produces error values for the concepts returned by ConceptWiki that are apparently not present in OPS (e.g. for "ezh2" and limit=10, it gives 7/10 error values vs "ezh2 (homo sapiens)" giving 2 valid values).

Created: 2013-06-18

Credits: User Marco Roos User Katy Wolstencroft User paul groth

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Blob A Method To Construct Gene Regulatory Networks To Es...

Created: 2013-06-10 06:56:01

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

S.P. Chai, M.S. Mohamad. A Method To Construct Gene Regulatory Networks To Estimate and Calculate Time Delay. (2013). Jurnal Teknologi. Vol. 62, No. 1, pp. 25-31. UTM Press. Indexed by SCOPUS. 

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Taverna 2
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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel

Workflow Biome-BGC MCE 1.4.1 (4)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models were implemented: Biome-BGC 4.1.1 MPI (Trusilova et al. 2009) and Biome-BGC MuSo 3.0 (Hidy & Barcza 2014). Its has about 40 and 60 various parameters. The only way to estimate or set these parameters is "calibration" (data-model-harmonization or model-data-fusion), which demands a hugh amount of computational capacity. Monte Carlo Exp...

Created: 2013-06-04 | Last updated: 2014-10-04

Credits: User Ferenc HORVATH User Zoltan BARCZA User Dora Krasser User Peter Ittzes Network-member BioVeL

Taverna 2
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1730?size=60x60 De cneudecker

Workflow Fraunhofer IAIS mydec (4)

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This workflow is provided by the Succeed EU project. For more information about Succeed, please visit http://succeed-project.eu/. For more information about mydec, please visit http://www.iais.fraunhofer.de/mydec.html

Created: 2013-06-04 | Last updated: 2014-02-07

Credits: User cneudecker

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Blob Identifying Minimal Genomes and Essential Genes in M...

Created: 2013-05-31 03:04:59

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A.H.M. Salleh, M. S. Mohamad, S. Deris, R. M. Illias, “Identifying Minimal Genomes and Essential Genes in Metabolic Model Using Flux Balance Analysis”, The 5th Asian Conference on Intelligent Information and Database Systems (ACIIDS 2013), Istana Hotel, Kuala Lumpur, Malaysia, 18-20 March, 2013

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Blob Multiple Gene Sets for Cancer Classification Using G...

Created: 2013-05-31 03:04:30

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

K. Moorthy, M.S. Mohamad, S. Deris, “Multiple Gene Sets for Cancer Classification Using Gene Range Selection Based on Random Forest”, The 5th Asian Conference on Intelligent Information and Database Systems (ACIIDS 2013), Istana Hotel, Kuala Lumpur, Malaysia, 18–20 March, 2013. 

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Blob Using Bees Hill Flux Balance Analysis (BHFBA) for in...

Created: 2013-05-31 03:03:51

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Y. W. Choon, M. S. Mohamad, S. Deris, R. M. Illias, L. E. Chai, “Using Bees Hill Flux Balance Analysis (BHFBA) for in silico Microbial Strain Optimization”, The 5th Asian Conference on Intelligent Information and Database Systems (ACIIDS 2013), Istana Hotel, Kuala Lumpur, Malaysia, 18-20 March, 2013. 

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Blob A Hybrid of Artificial Bee Colony and Flux Balance A...

Created: 2013-05-31 03:03:16

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

S.S Lee, Y.W. Choon, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, M.S. Mohamad, “A Hybrid of Artificial Bee Colony and Flux Balance Analysis for Identifying Optimum Knockout Strategies for Producing High Yields of Lactate in Echerichia Coli”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia, 27-28 February 2013. 

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Blob Identifying Gene Knockout Strategy Using Bees Hill F...

Created: 2013-05-31 03:02:36

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Y.W. Choon, M.S. Mohamad, S. Deris, R.M. Illias, L.E. Chai, C.K. Chong, “Identifying Gene Knockout Strategy Using Bees Hill Flux Balance Analysis (BHFBA) for Improving the Production of Ethanol in Bacillus Subtilis”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Prediction of Vanillin Production in Yeast Using a H...

Created: 2013-05-31 03:01:58

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

L.H. Yin, Y.W. Choon, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, M.S. Mohamad, “Prediction of Vanillin Production in Yeast Using a Hybrid of Continuous Bees Algorithm and Flux Balance Analysis (CBAFBA)”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Inferring Gene Networks from Gene Expression Data Us...

Created: 2013-05-31 03:01:03

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

M.A. Mutalib, L.E. Chai, C.K. Chong, Y.W. Choon, S. Deris, R.M. Illias, M.S. Mohamad, “Inferring Gene Networks from Gene Expression Data Using Dynamic Bayesian Network with Different Scoring Metric Approaches”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Using Particle Swarm Optimization for Estimating Kin...

Created: 2013-05-31 03:00:33

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

S.T. Ng, C.K. Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S. Shamsir, M.S. Mohamad, “Using Particle Swarm Optimization for Estimating Kinetics Parameters on Essential Amino Acid Production of Arabidopsis Thaliana”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Using Ant Colony Optimization (ACO) on Kinetic Model...

Created: 2013-05-31 03:00:05

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

N.F. Saidin, C.K Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S Shamsir, M.S. Mohamad, “Using Ant Colony Optimization (ACO) on Kinetic Modeling of the Acetoin Production in Lactococcus Lactis C7”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia,  27-28 February 2013. 

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Blob Inferring E. coli SOS Response Pathway from Gene Exp...

Created: 2013-05-31 02:59:33

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

L.E. Chai, M.S. Mohamad, S.Deris, C.K. Chong, Y.W. Choon, “Inferring E. coli SOS Response Pathway from Gene Expression Data Using IST-DBN with Time Lag Estimation”, International Symposium on Biomedical Data Infrastructure (BDI 2013), University of Malaya, Kuala Lumpur, Malaysia, 27-28 February 2013. 

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Blob A Hybrid of SVM and SCAD with Group-specific Tuning ...

Created: 2013-05-31 02:58:54

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

M.F. Misman, W.H. Chan, M.S. Mohamad, S.Deris, “A Hybrid of SVM and SCAD with Group-specific Tuning Parameters in Identification of Informative Genes and Biological Pathways”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Identifying Gene Knockout Strategy Using Bees Hill F...

Created: 2013-05-31 02:58:12

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Y.W. Choon, C.K. Chong, L.E. Chai, M.S. Mohamad, S.Deris, R.M Illias, “Identifying Gene Knockout Strategy Using Bees Hill Flux Balance Analysis  (BHFBA) for Improving the Production of Succinic Acid and Glycerol in Saccharomyces cerevisiae”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob A Constraint and Rule In an Enhancement of Binary Pa...

Created: 2013-05-31 02:57:36

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 M.S. Mohamad, S. Omatu, S. Deris, M. Yoshioka, “A Constraint and Rule In an Enhancement of Binary Particle Swarm Optimization To Select Informative Genes For Cancer Classification”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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Blob Multiclass Prediction for Cancer Microarray Data Usi...

Created: 2013-05-31 02:56:51

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

K. Moorthy, M.S. Mohamad, S. Deris, “Multiclass Prediction for Cancer Microarray Data Using Various Variables Range Reduction Based On Random Forest”, The First International Workshop on Data Analytics for Targeted Healthcare (DANTH 13), Gold Coast, Australia, 14-17 April 2013.

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