myExperiment - Content

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Matej MihelÄiÄ‡

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MovieLens data for hybrid recommenders

Created: 2012-05-17 11:04:57 | Last updated: 2012-05-17 11:06:10

Credits: tomS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is MovieLens data set containing user,item, ratings and item attributes enabling hybrid recommendation system testing.

File type: Trident (Package)

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Matej MihelÄiÄ‡

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Hybrid recommender RapidMiner and extension operators

Created: 2012-05-17 10:57:03 | Last updated: 2012-05-17 11:13:51

This pack contains workflow and data for hybrid recommender that is created by combining Recommender extension and RapidMiner built in operators.

2 items in this pack

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RapidMiner

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Ninoaf

Online update recommendation web service (1)

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After some arbitrary number of recommendations to specific users, system has to update recommendations in \textit{item recommendation table}. This is accomplished by calling the online update recommendation web service, which updates the recommendation model in RapidAnalytics repository and updates the recommendations for specific users in \textit{item recommendation table}.

Created: 2012-05-11 | Last updated: 2012-05-11

RapidMiner

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Ninoaf

Write activity web service (1)

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When the specific user $i$ "consumes" certain item $j$ the write activity web service is called, which writes activity $(i,j)$ to \textit{train set table} and removes recommendation $j$ for user $i$ from \textit{item recommendation table} in SQL database.

Created: 2012-05-11 | Last updated: 2012-05-11

RapidMiner

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Matija Piskorec

Execution time measurement for Rapidminer ... (1)

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This is a workflow that measures execution times of various RapidMiner operators on random polynomial classification datasets of various sizes in the range of 4 to 2000 examples and attributes.

Created: 2012-05-11 | Last updated: 2012-05-11

RapidMiner

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Ninoaf

Front-end Recommendation Web Service (1)

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Front-end recommendation web service has a simple job to query the cached recommendations from the \textit{item recommendation table}

Created: 2012-05-11 | Last updated: 2012-05-11

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Ninoaf

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Recommender system engine in RapidAnalytics

Created: 2012-05-11 12:54:44 | Last updated: 2012-06-20 14:47:43

Here we provide four workflows that build the recommender engine by using the recommender extension. The Recommender Extension can be downloaded from the Rapid-I Marketplace from: http://rapidupdate.de:8180/UpdateServer/faces/product_details.xhtml?productId=rmx_irbrecommender . More details can be found: http://elico.rapid-i.com/recommender-extension.html

9 items in this pack

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Mohd Saberi

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Prediction of Protein Residue Contact Using Support ...

Created: 2012-05-11 02:44:49

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Prediction of protein residue contact is one of the important two-dimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or noncontacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy o...

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Mohd Saberi

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Predicting Protein Secondary Structure with Neural N...

Created: 2012-05-11 02:34:20

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Protein secondary structure prediction has benefited largely from the improvements in machine learning techniques. A novel neural network classifier based on the Dempster-Shafer theory has been introduced by Denoeux. It demonstrated favourable performance in some artificial and real world problems when compared against methods such as Support Vector Machines and Kernel Fisher Discriminants. However, it has not been used for protein secondary structure prediction. In this work, we examin...

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Mohd Saberi

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Pathway-Based Microarray Analysis for Defining Stati...

Created: 2012-05-11 02:33:00

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In this reiew, we have discussed about approaches in pathway based microarray analysis. Commonly, there are two approaches in pathway based analysis, Enrichment Score and Supervised Machine Learning. These pathway based approaches usually aim to statistically define significant pathways that related to phenotypes of interest. Firstly we discussed an overview of pathway based microarray analysis and its general flow processes in scoring the pathways, the methods applied in both a...

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Mohd Saberi

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Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-05-11 02:28:43 | Last updated: 2012-05-11 02:28:44

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data which is used to simulate glycolysis pathway for Satcharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testified to be better than the other estimation algorithms. The outcomes from this study promot...

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Mohd Saberi

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Optimized Local Protein Structure with Support Vecto...

Created: 2012-05-11 02:27:24

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact 1fo1sngh complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental...

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Mohd Saberi

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One-Class Classifier to Predict Protein-Protein Inte...

Created: 2012-05-11 02:25:30

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Protein-protein interactions are important in a wide range of biological processes. The development of drugs that target such interactions is a very active research field. Hence predicting protein-protein interactions represent an important challenge in bioinformatics research. Machine learning techniques have been applied to predict protein-protein interactions. Most of these techniques address this problem as a binary classification problem. While it is easy to get a dataset of...

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Mohd Saberi

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Multi-Objective Optimization Using Genetic Algorithm...

Created: 2012-05-11 02:23:50

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Microarray technology has been increasingly used in cancer research because of its potential for measuring expression levels of thousands of genes simultaneously in tissue samples. It is used to collect the information from tissue samples regarding gene expression differences that could be useful for cancer classification. However, this classification task faces many challenges due to availability of a smaller number of samples compared to the huge number of genes, and many of ...

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Mohd Saberi

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Intelligent Hybrid Algorithm using Constraint-Based ...

Created: 2012-05-11 02:21:50

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Almost all hospital has its own nurses and still use the old fashion manual way of managing nurse scheduling in daily business. Nurse scheduling problem represents a difficult class of multi-objective optimisation problems consisting of a number of interfering objectives between the hospitals and individual nurses. Nurse scheduling consists of assignment of shifts and holidays to nurses for each day on the time horizon, taking into consideration a variety of conflicting interests or obj...

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Mohd Saberi

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Inferring Gene Regulatory Networks from Gene Express...

Created: 2012-05-11 02:20:28

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the ...

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Mohd Saberi

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Identifying Metabolic Pathway within Microarray Gene...

Created: 2012-05-11 02:18:43 | Last updated: 2012-05-11 02:18:44

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extracting metabolic pathway that dictates a specific biological response is cunently one of the important disciplines in metabolic system biology research. Previous methods have successfirlly identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structw€ is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identi&ing the significant...

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Mohd Saberi

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Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:16:43

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the lo...

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Mohd Saberi

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Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:15:08 | Last updated: 2012-05-11 02:15:09

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the lo...

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Mohd Saberi

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Genetic Algorithms Wrapper Approach to Select Inform...

Created: 2012-05-11 02:13:44

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Constantly improving gene expression technology offer the ability to measure the expression levels of thousand of genes in parallel. Gene expression data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. Key issues that need to be addressed under such circumstances are the efficient selection of minimum number of genes that contribute to a disease from the thousands of genes measured on microarrays that are inherently noisy. ...

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Mohd Saberi

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Feature Selection Method Using Genetic Algorithm for...

Created: 2012-05-11 02:10:56

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Practical pattern classification problems require selection of a subset of attributes or features to represent the patterns to be classified. The feature selection process is very important which selects the informative features for used classification process. This is due to the fact that performance of the classifier is sensitive to the choice of the features used to construct the good classifier from small or high dimension data that are inherently noisy. In this paper, we propose an...

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Mohd Saberi

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Distributed Data Partitioning Interface for Homogene...

Created: 2012-05-11 02:09:31

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The effort required to write efficient parallel programmes or to parallelize existing sequential algorithms remains daunting. This is true even for regularly structured problems. Much of the work takes place when partitioning and distributing workloads over processors in a distributed computing environment. To alleviate this task, we present a data parallel interface called Distributed Data Partitioning Interface (DDPI). Its simple interface permits parallel implementation even by users...

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Mohd Saberi

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Bioinformatics: A Tool for Bio-Knowledge Generation ...

Created: 2012-05-11 02:08:16

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

With the knowledge-based economy (KBE) emerging as a new paradigm, it becomes important that economic actors acquire new knowledge and technology. This will stimulate innovation and contribute further growth and development. In the knowledge-based economy, it is not tangible capital but intangible and innovations that determine international competitiveness, productivity growth and worker’s status in the labour market. This intangible capital and innovation are supplied by knowled...

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Mohd Saberi

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Automation of DNA Computing Readout Method Based on ...

Created: 2012-05-11 02:05:16

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Preaiausly, an eutornatian of a DNA mmputing rcodad methd far the HamiJtoni,an Path Prcblen (EPP) hos been implementd bosed on, LightCgcler Sgstem. In this stud,y, a simiJar reoilmrt approach is implemented baseil on DNA Engine Opticon 2 System. The rcadott appmaeh consists of tuo steps: rcnl-time arnplification in vitro us'i,ng TaqMowbaseil rcal-time PCR, followed by on in sili,co phase. The in silico phase consists of a d,ata clwtering algorithm and an information processing to e...

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Mohd Saberi

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Applying Filter Approach and Genetic Algorithm Wrapp...

Created: 2012-05-11 02:02:28

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Gene expression microarray data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. One problem arising from this data is how to select a small subset of genes from thousands of genes and much fewer samples that are inherently noisy. This research deals with finding a small subset of informative genes from the gene expression data which maximize the classification accuracy and minimize the running time. This paper proposed a mo...

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Mohd Saberi

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An Iterative GASVM-Based Method: Gene Selection and ...

Created: 2012-05-11 02:00:37

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Microarray technology has provided biologists with the ability to measure the expression levels of thousands of genes in a single experiment. One of the urgent issues in the use of microarray data is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult due to many irrelevant genes, noisy genes, and the availability of the small number of samples compared to the huge number of genes (hi...

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Mohd Saberi

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An Improved Binary Particle Swarm Optimisation for G...

Created: 2012-05-11 01:58:19

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The application of microarray data for cancer classification has recently gained in popularity. The main problem that needs to be addressed is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult because of the availability of the small number of samples compared to the huge number of genes, many irrelevant genes, and noisy genes. Therefore, this paper proposes an improved binary parti...

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Mohd Saberi

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An Image Registration Technique To Enhance PCB Inspe...

Created: 2012-05-11 01:56:19

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

is well k*atm that renl PCB inuge inipieetio* bwal 0n rclerential ap: proaches foces misalignment problems in detecting delects betwecn a template imoge arul a ilefectiae image. Hence, o reliable image registrtion techniqre is needed to aligt, these two irnages per{utly. Henre, a rqistrution trch*irye uhich inaryorvtes affme trcnsformotion anil bi-cubic interynlation has been prcposed. Etperimental rcsults haae shown that this regishation techniqte is suitoble to be employei to obt...

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Mohd Saberi

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A Two-Step Binary Particle Swarm Optimization Approa...

Created: 2012-05-11 01:52:33 | Last updated: 2012-05-11 01:52:34

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Manipitetibn of wdre itzing, buffer sizing, and futffer inseriiai atu a few techniques that con be used to i,mproae tfune d,eloy 'in aery lorge su,le intqrction (VLSI) circuit routing- Thi* paper enhances an eri,sting approach, which is based on Particl,e Swarrn Optimization (PSO) fur sofuing rcuting poblem in VLil circaits. A hoo-step Binary Particle Swarm Optimizatdon (BPSO) apprcach, which is based on BPSO, is chosen in thi^s stuily to improue time ilelay through finding the bes...

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Mohd Saberi

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A Study of Network-based Approach for Cancer Classif...

Created: 2012-05-11 01:49:20 | Last updated: 2012-05-11 01:49:21

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The advent of high-throughput techniques such as microarray data enabled researchers to elucidate process in a cell that fruitfully useful for pathological and medical. For such opportunities, microarray gene expression data have been explored and applied for various types of studies e.g. gene association, gene classification and construction of gene network. Unfortunately, since gene expression data naturally have a few of samples and thousands of genes, this leads to a biologi...

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Mohd Saberi

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A Parallelizing Interface for K-Means Type Clusterin...

Created: 2012-05-11 01:46:24

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The k-means clustering algorithm and neural network batch training becomes computationally intensive when the manipulated data is large. One way to reduce the computational demand of such techniques is to execute them in a concurrent manner. Unfortunately, the effort required to implement these techniques in a distributed computing environment remains daunting. Much of the work takes place when partitioning and distributing workloads over processors in the distributed computing environm...

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Mohd Saberi

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A New Hybrid Firefly Algorithm for Complex and Nonli...

Created: 2012-05-11 01:44:17 | Last updated: 2012-05-11 01:44:18

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Global optimization methods play an important role to solve many real-world problems. However, the implementation of single methods is excessively preventive for high dimensionality and nonlinear problems, especially in term of the accuracy of finding best solutions and convergence speed performance. In recent years, hybrid optimization methods have shown potential achievements to overcome such challenges. In this paper, a new hybrid optimization method called Hybrid Evolutionary ...

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Mohd Saberi

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

Created: 2012-05-11 01:39:36

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The incorporation of pathway data into the microarray analysis had lead to a new era in advance understanding of biological processes. However, this advancement is limited by the two issues in quality of pathway data. First, the pathway data are usually made from the biological context free, when it comes to a specific cellular process (e.g. lung cancer development), it can be that only several genes within pathways are responsible for the corresponding cellular process. Second, p...

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RapidMiner

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Matija Piskorec

Calibration for execution time extension (1)

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Benchmark workflow that loops Naive Bayes operator many times and provides estimate of the system's overall performance.

Created: 2012-05-10 | Last updated: 2012-05-10

Taverna 2

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Stian Soiland-Reyes

Extract DEC and RA from whitespace separat... (2)

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This workflow extracts DEC and RA coordinates from a whitespace seperated file and this is a silly description.

Created: 2012-05-10 | Last updated: 2012-09-24

Credits: Stian Soiland-Reyes

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Momo66323

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ir

Created: 2012-05-10 13:55:41

Credits: Momo66323

License: Creative Commons Attribution-Share Alike 3.0 Unported License

it test

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Ninoaf

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Dataset for Simple RS Web Service

Created: 2012-05-10 12:01:26 | Last updated: 2012-05-10 12:01:27

Credits: Ninoaf

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the dataset that is used by process: http://www.myexperiment.org/workflows/2901.html

File type: Trident (Package)

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RapidMiner

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Ninoaf

Simple Recommender System Web Service (1)

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This workflow takes macro value of user request and computes top-n recommendations from already learned model on train set. Macro value is transformed to example set with the appropriate \textit{user identification} role within \textit{ProcessInput} subprocess operator. Simple recommendation web service workflow takes three inputs: \begin{enumerate} \item Macro value \textit{user} - identification number of user request \item Train set from RM repository \item Learned Mo...

Created: 2012-05-10 | Last updated: 2012-05-10

Taverna 2

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Markus Plangg

Simple image migration (1)

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Then starts a migration action on an image and extracts properties from the original and migrated image. The properties are compared and a QA algorithms is started on the image data itself .

Created: 2012-05-08 | Last updated: 2012-05-08

Credits: Markus Plangg

Taverna 2

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Stian Soiland-Reyes

Find workflow ancestors (2)

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Given a t2flow file (Taverna 2 workflow), extract ancestor workflow UUIDs and search myExperiment for matching workflow entries. Note that this will also match the workflow itself and nested workflows, but does not match against other workflows having the same ancestors (but newer UUIDs).

Created: 2012-05-08 | Last updated: 2012-07-09

Credits: Stian Soiland-Reyes

Taverna 2

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Stian Soiland-Reyes

Check Java Cryptography Unlimited Strength (1)

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Checks if Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files is installed, and redirects user to correct download page and relevant lib/security folder if not.

Created: 2012-05-08 | Last updated: 2012-05-08

Credits: Stian Soiland-Reyes

Attributions: Find/show Taverna's home directory

Taverna 2

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BioCo Consultants

extractGInumber (1)

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This workflow uses regex pattern to compare the identity percentage of each hits against the input sequnece and return the whole information of the hits and the GI number of them (if they including the GI number as a sub information) inputfileURL: the location of the Gi number outputText : the list of all the hits and the GI number of them

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

Taverna 2

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BioCo Consultants

filterDifferenceInLists (1)

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This workflow output a list of the protein or any string hits in the first list but not in the second list. output : output file location com : comparision protein list our : interested protein list out1: output as a string

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

Taverna 2

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BioCo Consultants

ConcatStringTogether (1)

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This workflow is as simple as you can imagine! It can be used to remove the information tags in a fasta file and concat the sequence together fastaURL : the input fasta reads file location seqURL : the outcome sequence file location wholeSeq : the output sequence as an entire string

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

Taverna 2

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BioCo Consultants

generateWholeSeqAnnotation (1)

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This work flow is used for genereating all the known genes together to annotate a whole or a large region of genome sequence. outputfilrURL: the location of the output file Ginumber: the input gi gene number wholeGenomeSeq: the whold sequence annotation information output: the output of genbank text

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

Taverna 2

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BioCo Consultants

Get top blastx hit of a list of contigs (1)

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This workflow takes a contigs.fasta file , gets all the ORF's present in it , runs blastx on each ORF, gets the FASTA file of the top blastX hit and its GI number.

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

Taverna 2

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Georgeg9

FINAL VERSION (1)

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From genome to genbank file and annotations Manual and documentation at: http://www.students.ncl.ac.uk/g.georgiou/newweb/

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Georgeg9 BioGreen Ltd.

Attributions: Convert to KEGG ID NCBI Gi to Kegg Pathways EBI_NCBI_BLAST EBI_InterproScan_NewServices

Taverna 2

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Georgeg9

Run on amazon cloud (1)

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Execute commands on amazon cloud machines Manual and documentation at: http://www.students.ncl.ac.uk/g.georgiou/newweb/

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Georgeg9 BioGreen Ltd.

Taverna 2

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Junzhao

Search for Gene Expression Images using an... (1)

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This is a simple workflow demonstrating how to integrate multiple linked data sources using restful services in Taverna. In this workflow it first searches for all possible gene names for a query gene from FlyBase repository, an authorative genetic database for Drosophila research, and then it uses returned gene names to search for gene expression images from Oxford FlyTED image repository. Two Restful services were used: One for retrieving all flybase features matching a querying ge...

Created: 2012-05-04 | Last updated: 2012-05-08

Credits: Junzhao

Taverna 2

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Junzhao

Get Alternative Gene Names for a Drosophil... (1)

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This is a simple workflow testing running a restful service in Taverna. This restful service http://www.open-biomed.org.uk/service/flybase/features/name/{name} is part of the flykit/flybase services http://code.google.com/p/open-biomed/wiki/Flybase, which is built using the Talis Puelia Linked Data API (http://code.google.com/p/puelia-php/). We want to use this simple workflow to test the idea of bridging linked data and scientific workflows using Restful services. A test input gene name...

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Junzhao

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