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Open Access Research article

poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening

Raghunandan M Kainkaryam1 and Peter J Woolf1,2*

Author Affiliations

1 Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA

2 Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA

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BMC Bioinformatics 2008, 9:256 doi:10.1186/1471-2105-9-256

Published: 30 May 2008

Additional files

Additional file 1:

The MATLAB code used to implement the poolHiTS algorithm is provided. It includes the advances described in this paper, such as, the error-rate, mixing constraint and the block design strategy. This subroutine implements the standard STD decoding algorithm to identify the active compounds using the result T of a pooled experiment, M.

Format: M Size: 1KB Download file

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Additional file 2:

The MATLAB code used to implement the poolHiTS algorithm is provided. It includes the advances described in this paper, such as, the error-rate, mixing constraint and the block design strategy. This subroutine executes Algorithm 3 for a given set of parameters n, d, e, m to obtain the optimal values of q and k.

Format: M Size: 2KB Download file

Open Data

Additional file 3:

The MATLAB code used to implement the poolHiTS algorithm is provided. It includes the advances described in this paper, such as, the error-rate, mixing constraint and the block design strategy. This subroutine executes Algorithm 4 for a given set of parameters n, d, e, m, pB to choose the optimal block configuration of B and nB. It calls the poolHiTS-design.m and poolHiTS-hypgeo.m subroutines.

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Open Data

Additional file 4:

The MATLAB code used to implement the poolHiTS algorithm is provided. It includes the advances described in this paper, such as, the error-rate, mixing constraint and the block design strategy. This is the main file that needs to be executed, where the parameters n, d, e, m can be set and in-silico experiments can be run. It utilizes the poolHiTS.m subroutine for choosing the design, the poolHiTS-const.m subroutine for construction and the poolHiTS-decode.m subroutine for decoding the results of a pooled assay.

Format: M Size: 3KB Download file

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Additional file 5:

The MATLAB code used to implement the poolHiTS algorithm is provided. It includes the advances described in this paper, such as, the error-rate, mixing constraint and the block design strategy. This subroutine executes Construction 2 for a given set of parameters n, q and k.

Format: M Size: 1KB Download file

Open Data

Additional file 6:

The MATLAB code used to implement the poolHiTS algorithm is provided. It includes the advances described in this paper, such as, the error-rate, mixing constraint and the block design strategy. This subroutine evaluates the left hand side of Equation 2 for a given set of n, d, nB and dB.

Format: M Size: 1KB Download file

Open Data