文件列表:

BBioinfYeastzr\BioinfYeastzipCode\classifyotherscript.m (2964, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\classifyscript.m (2822, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\classifyscriptR.m (2810, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\ClassifySummary.m (2298, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\classify_other.m (7267, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\combinescript.m (2726, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\combineseedscript.m (2784, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\combine_fold.m (8541, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\combine_foldseed.m (5544, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\combine_fold_all.m (7473, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\combine_seed.m (8242, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\createfieldconfusionmat.m (1962, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\createnfoldrandperm.m (5005, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\createnfoldscriptR.m (1956, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\data\allOrfData.txt (758109, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\data\logisparam.mat (54737, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\data\schemarr.txt (1476, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\data\subcellulardata.txt (666223, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\fig345.m (2880, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata.m (1575, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata0.m (1892, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata1.m (1264, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata1_clusterv1.sh (246, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata2.m (1482, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata2_clusterv1.sh (246, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata3.m (1266, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata3_clusterv1.sh (246, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata4.m (1151, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata4_clusterv1.sh (155, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5.m (3351, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_classifyscriptFlag3R.sh (1779, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_combinefoldcriptFlag3.sh (1729, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_combinefoldcriptFlag41.sh (1955, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_combinefoldcriptFlag42.sh (1955, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_combineseedcriptFlag3.sh (329, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_combineseedcriptFlag41.sh (330, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_combineseedcriptFlag42.sh (330, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata5_createnfoldscriptFlag3.sh (1646, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata6.m (1084, 2007-11-05)
BBioinfYeastzr\BioinfYeastzipCode\makedata6_clusterv1.sh (155, 2007-11-05)
... ...

README This distribution contains all the codes and data for the work described in Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, and Robert F. Murphy. Automated Image Analysis of Protein Localization in Budding Yeast. Bioinformatics 23:i66-i71, 2007. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. For additional information visit http://murphylab.web.cmu.edu or send email to murphy@cmu.edu ====== Instructions for running the simulations and generating the figures in the paper ================================================================== Image Preparation The yeast image collection can be downloaded from http://yeastgfp.ucsf.edu/ Please make a directory D (Ex: '/etc/tmp') to store these images first. To download the images, first copy yeast_image_download.pl and yeast_image_download.txt to D. 1) Run 'perl yeast_image_download.pl' for downloading. 2) After the downloading is finished, run 'untargz.sh' to unzip the files. 3) Specify the yeastRoot variable in make_procfile.m % yeastRoot is the Root directory where the images are stored % Default value: yeastRoot = '/images/yeastGFP'; After this, you are ready to perform downstream analysis. ================================================================== Option 1: If using a single computer: Run "makedata.m" to generate all the data and results === Option 2: If using a computer cluster: The analyses in makedata.m are divided into a number of scripts so that each can be run on a different machine (e.g., in a Beowulf cluster environment). There are several script which need a lot of computaions as following: 1. makedata1.m for image segmentation 2. makedata2.m for cell level feature calculation 3. makedata3.m for field level feature calculation 4. makedata4.m to load features for cell level classification 5. makedata5.m for cell level classification with purality voting scheme 6. makedata6.m to load features for field level classification 7. makedata7.m for field level classification 8. makedata8.m for creating tables and figures in the paper In this case, makedata0.m should be run first to generate yeastdata.mat and procfiles.mat (under ./data) which contains yeast image path and UCSF localization categories and labels After the data have been generated, makedata1 through makedata7 can be run on separate nodes to generate the results (e.g. using "sh makedata1_clusterv1.sh", "sh makedata2_clusterv1.sh", "sh makedata3_clusterv1.sh" ,"sh makedata4_clusterv1.sh, "sh makedata6_clusterv1.sh" and "sh makedata7_clusterv1.sh"). Note that, scripts related to cell level classification of 25 seeds(in makedata5.m) should be executed in the following order: (1) sh makedata5_createnfoldscriptFlag3.sh Usage: Create index file: it takes about one hour for each seed, which this should be done first. (2) sh makedata5_classifyscriptFlag3R.sh Usage: Do classification on 20 class: it takes about 7*6 hours per seed, which can run after index files have been created. (3) sh makedata5_combinefoldcriptFlag3.sh Usage: Combine results from each fold per seed: it does not take long, which can run after classification results are available. (4) sh makedata5_combineseedcriptFlag3.sh Usage: Combine results from each seed: it takes about 10 minutes, which can run after each classification fold is combined. (5) sh makedata5_combinefoldcriptFlag41.sh Usage: Do classification on ambiguous class: it takes about two hour per seed, which can run after classifiers are trained. (6) sh makedata5_combinefoldcriptFlag42.sh Usage: Do classification on punctate_composite class: it takes about one hour per seed, which can run after classifiers are trained. (7) sh makedata5_combineseedcriptFlag41.sh Usage: Combine results from each fold and each seed: it takes about 10 minutes, which can run after each classification fold is combined. (8) sh makedata5_combineseedcriptFlag42.sh Usage: Combine results from each fold and each seed: it takes about 10 minutes, which can run after each classification fold is combined. Also, scripts related to field level classification should be executed in order after the all the images have been processed. (e.g. you have to finish the field level feature calculation before you do the field level classification). Lastly, "makedata8.m" should be executed generate the tables and figures. === The UCSF yeast location category and lables: The file allOrfData.txt (under ./data) contains the UCSF yeast location category and lables and can be downloaded from http://yeastgfp.ucsf.edu/allOrfData.txt === The CYGD yeast location category and lables: There are two files for assigning the labels: data/schemarr.txt and data/subcellulardata.txt The file schemarr.txt (downloaded from ftp://ftpmips.gsf.de/yeast/catalogues/subcellcat/subcellcat.scheme) contains two columns. The first column contains the location numbers and the second column contains the location names. The function tz_loadlocschm can be used to parse this file. The file subcellulardata.txt (downloaded from ftp://ftpmips.gsf.de/yeast/catalogues/subcellcat/subcellcat_data_14112005) contains information about ORFs. Each row has the structure like: ORF_NAME|LOCATION_LABEL|...|... The function tz_loadlocdata is for parsing this file. Given any image file name, you need to extract ORF name first. Then search ORF name in subcellulardata.txt to get its location label. For example: filepath = '/images/yeastGFP/ChrXVI/YPR191W_ver00-A-2000ms_GFP.png'; orf = tz_getgenename(filepath); %it will return 'YPR191W' locs = tz_loadlocdata('data/subcellulardata.txt'); index = strmatch(orf,locs.geneNames,'exact'); label = locs.locationLabels{index}; ====== A MATLAB LIBSVM Toolbox is used in this work (under ./SLIC/classify/libsvm). The toolbox is Copyright (c) Chih-Chung Chang and Chih-Jen Lin, LIBSVM : a library for support vector machines, 2001 This software is available at http://www.csie.ntu.edu.tw/~cjlin/libsvm/ A SLIC (Subcellular Localization Image Classifier) toolbox is also used in this work (under ./SLIC) This software is available at http://pslid.cbi.cmu.edu/release/

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