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From: 焦娜 <jia...@16...> - 2017-04-12 13:02:04
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hello, I want to use ESOM for my phd project. But I have trobles in installing ESOM-1.1 the maven-1.0.2 have installed but when execute "maven jar install" it report errors How can I solve it? Thank you! -- Best regards! |
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From: Taruna A. <ta...@wi...> - 2016-11-23 01:42:01
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Hello, I’m trying to visualize our reads using ESOM with the help of this tutorial on Github <https://github.com/tetramerFreqs/Binning>. I prepared the files using the wrapper script from this tutorial. After loading the data into the GUI, we were getting just a white screen with one tiny dot (after training the dataset in the Databionics GUI). Then I tried to manually train the data using the esomTrain.pl script, but the output of that script did not appear to be in the correct format for loading into the GUI. Do you have any advice? Thanks for your help in advance! Taruna |
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From: <re...@pk...> - 2015-12-30 23:57:19
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Hi Reinhard Thanks for your quick reply. Great! I will download the files and follow the steps. Have a nice 2016!! Renato Koenig escreveu: > Download the files > > http://sourceforge.net/projects/databionic-esom/files/ [2] > > and follow the installation guides: > > http://databionic-esom.sourceforge.net/install.html [3] > > It's a bit tricky, but after a while I found how to do it… > > Good luck and best regards > > Reinhard > > Jun.-Prof. Dr. Reinhard König > > -------------------------------------------------------------- > > Senior Assistant & Lecturer | Chair of Information Architecture | ETH Zurich > > Wolfgang-Pauli-Strasse 27, HIT H 31.6, 8093 Zurich, Switzerland > > Phone: +41 44 633 72 10 | Fax: +41 44 633 15 75 | Mobile: +41 79 127 25 12 > > rei...@ar... | http://www.ia.arch.ethz.ch/koenig/ [4] > > -------------------------------------------------------------- > > Junior-Professor for Computational Architecture | Bauhaus-University Weimar > > Belvederer Allee 1, 99423 Weimar, Germany > > Phone: +49 3643 58 4210 | Fax: +49 3643 58 4202 | Mobile: +49 179 667 9978 > > rei...@un... | https://www.uni-weimar.de [5] > > -------------------------------------------------------------- > > FROM: re...@pk... [mailto:re...@pk...] > SENT: Mittwoch, 30. Dezember 2015 22:03 > TO: dat...@li... > SUBJECT: [Databionic-ESOM-User] Access to ESOM > > Dear sirs, > > I woud like to eccess ESOM software to support my post-doctorate studies. > > How can I do it please? > > Thanks and best regards > > Dr.Renato Neto > > ------------------------------------------------------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user [1] Links: ------ [1] https://lists.sourceforge.net/lists/listinfo/databionic-esom-user [2] http://sourceforge.net/projects/databionic-esom/files/ [3] http://databionic-esom.sourceforge.net/install.html [4] http://www.ia.arch.ethz.ch/koenig/ [5] https://www.uni-weimar.de/ |
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From: Reinhard K. <ko...@en...> - 2015-12-30 21:59:50
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Download the files http://sourceforge.net/projects/databionic-esom/files/ and follow the installation guides: http://databionic-esom.sourceforge.net/install.html It’s a bit tricky, but after a while I found how to do it… Good luck and best regards Reinhard Jun.-Prof. Dr. Reinhard König -------------------------------------------------------------- Senior Assistant & Lecturer | Chair of Information Architecture | ETH Zurich Wolfgang-Pauli-Strasse 27, HIT H 31.6, 8093 Zurich, Switzerland Phone: +41 44 633 72 10 | Fax: +41 44 633 15 75 | Mobile: +41 79 127 25 12 <mailto:rei...@ar...> rei...@ar... | <http://www.ia.arch.ethz.ch/koenig/> http://www.ia.arch.ethz.ch/koenig/ -------------------------------------------------------------- Junior-Professor for Computational Architecture | Bauhaus-University Weimar Belvederer Allee 1, 99423 Weimar, Germany Phone: +49 3643 58 4210 | Fax: +49 3643 58 4202 | Mobile: +49 179 667 9978 <mailto:rei...@un...> rei...@un... | <https://www.uni-weimar.de/> https://www.uni-weimar.de -------------------------------------------------------------- From: re...@pk... [mailto:re...@pk...] Sent: Mittwoch, 30. Dezember 2015 22:03 To: dat...@li... Subject: [Databionic-ESOM-User] Access to ESOM Dear sirs, I woud like to eccess ESOM software to support my post-doctorate studies. How can I do it please? Thanks and best regards Dr.Renato Neto |
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From: <re...@pk...> - 2015-12-30 21:33:18
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Dear sirs, I woud like to eccess ESOM software to support my post-doctorate studies. How can I do it please? Thanks and best regards Dr.Renato Neto |
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From: <re...@pk...> - 2015-12-30 21:20:27
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Dear sirs, I need to access Databionic software to support my post-doctorate studies Is it possible? Thanks and regards Dr. Renato Neto |
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From: Anders L. <and...@ic...> - 2015-07-01 08:28:29
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Hi. I am currently using ESOM for bioinformatical purposes and have been getting very nice results with it. I have 2 small questions that I hope somebody might be able to help with. 1. Regarding the Robust ZT transformation. Is there a way to get the exact formula used for this Z-transformation? I'm currently interested in setting up a command-line workflow for ESOM, and while I can run the training using 'esomtrn', it would be nice to have a GUI independent way to also do the Robust ZT transformation of the data. If there is a specific formula used I could make a small R-script for this and use it as a pre-processing step. 2. When changing the background in the viewer, my computer tends to freeze up, sometimes for quite a while if it is a big dataset. Is it possible to change the default background, since it always reverts back to the Umatrix when you reload the .wts file. Regards //Anders |
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From: <ire...@gm...> - 2014-09-19 19:39:26
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Hi, ire...@gm... wants to follow you. ****** Is ire...@gm... you friend? ****** If Yes please follow the link below: http://invites.info-emailer.com/signup_e.html?fullname=&email=dat...@li...&invitername=ire...@gm...&inviterid=30835192&userid=0&token=0&emailmasterid=c743d53a-547e-4d4f-af93-55905373d7a3&from=ire...@gm...&src=txt_yes If No please follow the link below: http://invites.info-emailer.com/signup_e.html?fullname=&email=dat...@li...&invitername=ire...@gm...&inviterid=30835192&userid=0&token=0&emailmasterid=c743d53a-547e-4d4f-af93-55905373d7a3&from=ire...@gm...&src=txt_no Follow the link below to remove yourself from all such emails http://invites.info-emailer.com/uns_inviter.jsp?email=dat...@li...&iid=c743d53a-547e-4d4f-af93-55905373d7a3&from=ire...@gm... |
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From: Dawn <daw...@gm...> - 2014-07-22 14:15:49
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Hi, *It's my first time to use ESOM, and I typed "./esomana" and got the following:* ------------------------------ Loading modules... Loading module Clustering Loading empty project... Loading project null Searching for Gradients Found 21 Gradients Searching for Parameters Searching background renderers databionics.esom.renderer. background.UMatrixRenderer databionics.esom.renderer.background.RandomRenderer databionics.esom.renderer.background.GapRenderer databionics.esom.renderer.background.TwoMatchRenderer databionics.esom.renderer.background.ComponentRenderer databionics.esom.renderer.background.SmoothedDataHistoRenderer databionics.esom.renderer.background.OpinionRenderer databionics.esom.renderer.background.PMatrixRenderer UMatrix Random Gap TwoMatch Component SmoothedDataHisto Opinion PMatrix Searching foreground renderers Bestmatch OpinionBestmatch Names Line ------------------------- There is no response any more. My system is Unix. Thank you very much! Dawn |
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From: Michael D. J. <mic...@ya...> - 2013-03-28 14:27:42
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http://www.farmershail.com/shaikv/wcvahnkwwpmgvenhtdravppt.qshquhrec |
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From: Lizzy W. <egw...@uc...> - 2013-03-11 20:25:43
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Hi there folks, I'm trying to run ESOM training on a large dataset and am running into issues with the java memory allocation. When I begin my k-batch training it gives the following error while trying to load the .lrn file: out of memory, try adjusting -Xmx in esomstart[.bat] (Java heap space) I edited a line in the esomstart script to read as follows, and have also tried higher memory allocations (up to -Xmx10240m): java -cp "$CP" -Xmx1024m $MAIN "$@" Sadly, this doesn't seem to be changing how the program runs, as it uses only about 500Mb of memory and then stops with the error. Am I editing the right file to change the memory allocation? Does something else need to be changed as well? I have tried running both from the command line with esomtrn and using the GUI via esomana. Any suggestions would be much appreciated! Thanks! Lizzy -- "The obvious goal of any bacterium is to become bacteria." Lizzy Wilbanks Graduate Student, Eisen and Facciotti Labs UC Davis, Microbiology Graduate Group |
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From: Michael D. J. <mic...@ya...> - 2013-03-06 12:11:35
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ruc hnyu http://www.christfellowshipny.com/hlavd/iva/wdymefcq/utfojjrdr wexhlhezeann mbsqlrjlzmj jv slawjvxeihp |
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From: <am...@ls...> - 2012-11-06 23:01:53
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Hi, I am using ESOM tools 2D and I am interested in 3D but I don't know if they exist. Can anybody tell me anything? Thanks in avanced. Àngela |
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From: Jennifer B. <jd...@gm...> - 2012-08-09 16:36:55
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Hi all, I am currently trying to download the databionics esom tool on windows 7. When trying to open the esom analyzer I get a command prompt window with the message "please initialize the log4j system properly". Any help with this at all would be great Thanks Jennifer |
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From: Jennifer B. <jd...@gm...> - 2012-08-08 13:21:36
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Hi, I am currently looking to compare ESOMS to traditional clustering methods. I am also particularly interested in investigating how to choose the "right" number for k. I have very minimal coding skills so was hoping your software could be used. I do however have to be able to access the code in order for the topic to be approved by my supervisor. Also if there are any particular areas in relation to ESOMs that are underdeveloped with regards to academic research & testing I would be interested in pursuing it as my research topic. Any advice would be appreciated Thanks Jennifer |
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From: irem d. <ire...@gm...> - 2012-04-04 09:41:04
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Hi, I try to install esom-1.1-installer on Windows 7 and have problems. I have examined the archieves of the mailing list and seen some similar problems. However I could not find any answers in the archieve. Could you help me? The problems are: 1.) The installation cannot be made on C: even with administrator privileges. I made the installation on D: but there was no shortcut or anything that enables to reach the Esom analyzer even if I selected shortcut path during installation. 2.) I tried to use esom-toolbox in Matlab. Bin is added to path. When esom_demo was run, a window as shown below appears: ------------------------------------------------------------------------------------------------------------------------------------------ 16 bit MS-Dos Subsystem Error while setting up environment for the application. Choose 'Close ' to terminate the application. ------------------------------------------------------------------------------------------------------------------------------------------- When close selected, below lines appear on Matlab command window and program terminates: D:\esom>call java -cp "D:\esom\lib\lshtools-0.9.9.jar;D:\esom\lib\log4j-1.2.8.jar;D:\esom\lib\gnu-regexp-1.1.4.jar;D:\esom\lib\esom-1.1.jar;D:\esom\lib\commons-cli-1.0.jar;D:\esom\lib\colt-1.2.0.6.jar;D:\esom\lib\ant-1.5.3-1.jar;" -Xmx512m databionics.esom.Train %* configuration file not found: D:\etc\esom.conf log4j:WARN No appenders could be found for logger (databionics.Application). log4j:WARN Please initialize the log4j system properly. ??? Error using ==> loadwts at 41 loadwts: could not open file demo.wts Error in ==> esom_train at 164 wts = loadwts([prefix, '.wts']); Error in ==> esom_demo at 61 [wts, bm, umx] = esom_train(NOData, prefix, epochs, rows, columns, grid, radius, learn, algorithm); What can I do to open the analyzer and use toolbox? Thanks in advance. İrem Hilavin Phd Student in EEE Dokuz Eylül University İzmir/TURKEY |
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From: Tali Raveh-S. <tal...@gm...> - 2012-03-12 20:02:03
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Hi, I would like to use ESOMs for an application in which I have ~1000 points (that are ~250 dimensional). From the manual I understood that one should use few thousands of neurons. Wouldn't that lead to overfitting? If not, why so? I read in some of Ultsch's papers that increasing the number of neurons does not directly increase the number of free paprameters since there are still the toplogy constraints, but is this true also when the ration of data points to neurons is more than 1:4? why? Thanks Tali |
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From: Marcelo L. <mar...@gm...> - 2012-02-27 03:11:29
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Hi All, I have a SOM trained by the Databionics ESOM tool. I also have a set of data that I need to run against this network to see which of the neurons of the network are activated by this set, but naturally many of the activated neurons are not the best matches. How can I determine the closest best match of the an activated neuron? I'm trying to create classes the way the help site says, but I'm not having success with that. Another option is to force the projection algorithm to only activate the best match neurons, I'm using the 'esomprj' tool, is there any way to do this? Thank you in advance. -- Marcelo Lotif. |
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From: Sebastian R. <seb...@ra...> - 2011-02-11 14:20:44
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Dear all, is there a possibility to display the names of the bestmatches using (command line tool) esomrnd? Best wishes, Sebastian Radestock. ============================================= Dr. Sebastian Radestock Computational Structural Biology Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main, Germany Tel: +49 (0)69 6303 1603 Cell: +49 (0)176 6407 2224 URL: http://www.radestock.net ============================================= |
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From: Chris P. <chr...@fm...> - 2011-01-06 01:18:57
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FLDAYTNA,FLJACKSV,FLMIAMIB,FLORLAND,FLTALLAH,FLTAMPA,FLWPALMB 78.2,74.8,79,77.1,76.6,80.4,78.8 77.6,77.4,78.9,77.8,78.2,80.2,80.2 78.7,77.5,78.5,79.6,81.3,79.5,78.2 78,76.6,80,77.4,84,80.3,79.9 77.5,78,81,76.9,77.7,79.2,79.6 80.4,77.3,81.2,77.7,79.4,79.8,81.5 79.7,76.5,80.7,75.8,77.3,79.5,78.6 79.8,75.2,77.3,76.4,79,78.5,74.9 80.3,73.9,81,77.6,78.7,79.3,79.4 77.4,77.3,83,77.9,78.8,78.8,80.5 77.9,76.2,81.3,79.4,76.2,83.1,79 79,76.2,79,78,76.6,81.8,77.3 |
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From: jcanistrum <jca...@gm...> - 2010-06-03 12:41:49
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Hi,
after using Pär Matsson tip for correcting esomstart.bat for Windows Vista
I.e., the last line of esomstart.bat should read:
call java -cp "%LOCALCLASSPATH%" -Dos.name=Windows.XP -Xmx512m
%MAIN% %%*
(
<http://sourceforge.net/mailarchive/forum.php?thread_name=000d01c9e3f7$beb30
3c0$3c190b40$%40matsson%40ucsf.edu&forum_name=databionic-esom-user>
http://sourceforge.net/mailarchive/forum.php?thread_name=000d01c9e3f7$beb303
c0$3c190b40$%40matsson%40ucsf.edu&forum_name=databionic-esom-user)
I got the demo running, but at the end it gave me this error message :
call "$INSTALL_PATH"\bin\esomstart.bat databionics.esom.Matrix %*
The system cannot find the path specified.
??? Error using ==> loadumx at 38
loadumx: could not open file demoComp.umx
Searching for the files created by esom_demo, I found demoPmatrix.umx and
demo.umx, but not demoComp.umx.
Anyone knows if demo.umx is the right one or something else is missing here?
Thanks in advance
Joao Carlos
MSc. student at IME-RJ
Brazil
|
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From: Fabian M. <fa...@my...> - 2010-04-25 01:01:56
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Peter, for ESOM (and many other data mining algorithms) you need a vector of numbers of a fixed length and a distance function. Based on your description. a very simple apporach would be to use 1 for present, 0 for absent, and euclid for the distance measure. for each student a vector of length 5x(weeks in semester) would need to be generated. for file formats please refer to the manual. if you want to capture the reason for absence it gets a bit more tricky. the letters are categories and not easily encoded in a single number. here it seems your 5 categories do have an ordering so you could use 0,...,4 or 0, 0.2, ..., 1 for present, ..., unjustified. similar vectors, thus attendance patterns, should be close on the map. you can investigate clusters to see what the typical patterns is inside them. best fabian Peter Sim wrote: > > Hi everyone > > > > I am *very new* to Emergent Self-Organizing Maps. > > > > My area of reseach encompasses school absenteeism. I have a year of > attendance data for several thousand students on a class-by-class > basis. The data looks like this (five classes per day): > > > > Student# Week Mon Tue Wed Thu Fri > > 1234 2/2/09 ***** ****T ***** EEEEE ***** > > 9/2/09 ***** JJJ** ***** L**LL ***** > > 16/2/09 ***** ***** ***SS ***** ***** > > ...etc > > 9876 2/2/09 ***** MMMMM ***** ***** ***** > > 9/2/09 ***** ***** ***** ***** QQQQQ > > 16/2/09 DDD** ***** ***** ***** ***** > > ...etc > > > > An asterisk indicates that the student is present. Letter codes > indicate the type of absence: D (Doctor/Dentist), E (Explained but > unjustified), J (Justified), L (present but Late), M (Medical), Q > (school trip or camp), T (Truant). > > > > I intend coding the attendances/absences into: > > -Present > > -Late > > -Justified (eg other school activity) > > -Justified but questionable (eg note from home stating student is unwell) > > -Unjustified (E and T) > > > > I want to examine a number of hypotheses about relationships between > individual students' attendance patterns early in the year, and later on. > > > > My supervisor has asked me to investigate whether ESOMs will be a > useful analytical tool in my research. I have downloaded and installed > the Databionic ESOM Tools. > > > > I'm having trouble figuring out how to preprocess my data into a > format suitable for use with the software. > > > > Can anyone point me in the right direction? > > > > MTIA > > > > Peter Sim > > New Zealand > > > > __________ Information from ESET Smart Security, version of virus > signature database 4906 (20100301) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ------------------------------------------------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > |
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From: Momodou L. S. <ml_...@ho...> - 2010-03-12 10:09:37
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Dear Sirs, I am currently working on a project of visualizing data using SOM. I am able to show the result in U-Matrix, but i could not show it in P-Matrix and U*-Matrix. I read your paper entitle "Maps for the Visualization of high-dimensional Data Spaces" and thoug you could be of help to me with the P-Matrix and U*-Matrix functions. I am using matlab 7.0 on a windows Xp. I did not have a toolbox which contains these functions. I am humbly seeking assistance from you in getting the P-Matrix and U*-Matrix functions. Do you know how i can get them? Can you please help me on these functions. Best Regards, Lamin _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969 |
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From: Richard P. <rhp...@gm...> - 2010-03-11 21:46:16
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had installed and used under NT. Trying to install on a new machine with W7 Pro. Have installed Java SDK 5. The downloaded esom code cannot be stored on the machine. I get the message "this directory cannot be written. Please choose another directory". How should I proceed? -- Richard Palmer Home 508 877-3862 Cell 508 982-7266 |
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From: Richard P. <rhp...@gm...> - 2010-03-11 21:41:46
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had installed and used under NT. Trying to install on a new machine with W7 Pro. Have installed Java SDK 5. The downloaded esom code cannot be stored on the machine. I get message -- Richard Palmer Home 508 877-3862 Cell 508 982-7266 |
2 messages has been excluded from this view by a project administrator.
