Activity for Toxtree: Toxic Hazard Estimation
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Stephen Bond created ticket #97
QSAR6,8 No Class Error
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Jeff Lohre posted a comment on discussion [Toxtree plugin] Carc/Mut
Any suggested fix for this issue? Jeff From: discussion@toxtree.p.re.sourceforge.net discussion@toxtree.p.re.sourceforge.net On Behalf Of Cheryl Marker Sent: Tuesday, January 31, 2023 9:24 AM To: [toxtree:discussion] 867722@discussion.toxtree.p.re.sourceforge.net Subject: [toxtree:discussion] Re: Problems getting data I am having the same issue with the same version Problems getting data https://sourceforge.net/p/toxtree/discussion/867722/thread/c648fb219f/?limi t=25#1db2/fe6e Sent from sourceforge.net...
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Cheryl Marker posted a comment on discussion [Toxtree plugin] Carc/Mut
I am having the same issue with the same version
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For the last at least a month, I have had a problem typing in a CAS No. into the "Chemical id" line and getting information. It only comes back with a reply "CAS entered, failed to retrieve from remote server". I have tried queeries that have run before successfully and they are not currently getting any ToxTree information. I have tried multiple times over the last month. The remote query option is selected. I am using Version v3.1.0.1851 Any suggestions?
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Nina Jeliazkova committed [769743]
versions update
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4.1.0-SNAPSHOT
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repositories and compiler settings cleanup
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Hyeran Park posted a comment on discussion Open Discussion
Dear. Toxtree inventors, Hello, I've used Toxtree online for searching and classifying lots of chemicals. However, some of them was not popped up for classification as well as their structures or any information about them. So, if I send to you their information including CAS number and chemical structures or something else, would you upload them into Toxtree for users? I'm looking forward to hearing from you soon. Thank you so much and have a lovely day. Respectfully, Hyeran Park
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https for mvn repos
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Luchesar ILIEV modified ticket #96
Toxtree will not open
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Hi Kim, Hope you're doing well! :) It was really such great news to hear that the new Windows 10 installation had fixed the problems with Toxtree for you! Have you had any further or new problems since then? While Toxtree, as a Java application, tends to work smoothly regardless of what operating system it runs on, and we haven't expected or noted specific problems with Windows 10, your experience will also be very valuable. Regarding the online version, you're correct! We've been planning on adding...
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Kim Li posted a comment on ticket #96
Hi Luchesar, Thank you so much for your email. Our IT rolled out Windows 10 updates this week and I decided to repeat all the instructions you've given me. And what a pleasant surprise, I now have the latest Toxtree version on my desktop! The online version works but it'll take time for me to navigate the features. I have not been able to find the "?" for online help LOL. Again, thanks so much for your excellent support. Best regards, Kim From: Luchesar ILIEV luchesar@users.sourceforge.net Sent:...
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Hi, Kim! Thank you very much for your understanding! I must say that I also very much sympathize with you... Indeed, the very fact that, apparently, Toxtree is so useful in your work, is one of the things that motivates us and keeps us going! This really means a lot to us! I'm also sorry that my previous reply must've sounded cold and maybe even unconcerned. This was a really peculiar problem that almost certainly had to do with some security policy that only the IT support could have helped with....
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Hi Luchesar, I understand and you have given me tremendous support. I just learned there is the online Toxtree version. It has a different look and feel and I need to become proficient soon. Thanks. Kim From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Thursday, February 25, 2021 7:55 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] #96 Toxtree will not open Hi Kim, It's been quite a busy time here, sorry. I can't help but say as well that here...
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Hi Kim, It's been quite a busy time here, sorry. I can't help but say as well that here we're effectively doing the job of your IT department. Which is something we could do, of course, but we do usually charge the people for such support, because it doesn't in any way help the development of our software. It's general IT support—not solving a problem with our software. Anyway, since we do generally try to help whenever we can, here's the situation... I don't know how you managed to end up with a...
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Hi Luchesar, I hope you are doing well. Can you help me getting to the finish line? I have been sharing your notes with my IT tech support but unable to get further help. Kim From: Li, Kim Sent: Thursday, February 11, 2021 5:01 PM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net; Luchesar ILIEV luchesar@users.sourceforge.net Subject: RE: [External] [toxtree:bugs] Re: #96 Toxtree will not open Hi Luchesar, Getting very close. I can only copy (not extract) the attachment to the directory created...
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Hi Luchesar, Getting very close. I can only copy (not extract) the attachment to the directory created but not sure what app to use to open it. Please see screen shots in attachment. Thanks. Kim From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Thursday, February 11, 2021 3:21 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] Re: #96 Toxtree will not open Hi Kim, It seems there's something preventing Toxtree from installing a dynamic-link library...
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Hi Kim, It seems there's something preventing Toxtree from installing a dynamic-link library that it needs for operation. It may be some administratively imposed policy by your IT—it's hard to tell. Here's one very crude attempt to solve this: 1. Open a command prompt. 2. Type md C:\Users\lik\.jnati\repo\jniinchi\1.03_1\WINDOWS-X86 and press Enter. This should create the required directory. 3. Confirm that the directory has been created by dir C:\Users\lik\.jnati\repo\jniinchi\1.03_1\WINDOWS-X86...
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Hi Luchesar, Got error message below Kim [cid:image001.jpg@01D6FE0B.998E8D40] From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Monday, February 8, 2021 4:58 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] Re: #96 Toxtree will not open Hi Kim, Could you please show the output of dir C:\Users\lik.jnati\repo\jniinchi\1.03_1\WINDOWS-X86\JniInchi-1.03_1-WINDOWS-X86.dll ? Thanks! [bugs:#96]https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Ftoxtree%2Fbugs%2F96%2F&data=04%7C01%7Clik%40amgen.com%7Cf3d3ca0b4cc542c6b10008d8cc3123ed%7C4b4266a6136841afad5a59eb634f7ad8%7C0%7C0%7C637483859484370623%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=nu%2BS2PRW3UPIOl981f7qqctX%2BKmSI%2FmQjf2wOB%2BbTf4%3D&reserved=0...
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Hi Kim, Could you please show the output of dir C:\Users\lik\.jnati\repo\jniinchi\1.03_1\WINDOWS-X86\JniInchi-1.03_1-WINDOWS-X86.dll ? Thanks!
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Hi Luchesar, Thanks for staying with me. Below is the Java version: [cid:image003.jpg@01D6FBD2.D6352780] Below is the Java location: [cid:image004.jpg@01D6FBD2.D6352780] Below is the screenshot when I run the Command prompt. The error message is so long, I put it in Word (attached). [cid:image005.jpg@01D6FBD2.D6352780] From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Friday, February 5, 2021 12:34 PM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs]...
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Could you please try java -jar Toxtree-3.1.0.1851.jar instead of javaw -jar Toxtree-3.1.0.1851.jar (the only difference is java in lieu of javaw)? Also, could you please provide the output of java -version?
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Hi Luchesar, I think I'm getting close but the program won't launch. Please take a look at the screenshot below and let me know what I am missing. Thanks. Kim [cid:image003.jpg@01D6FA41.EDD6BDA0] From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Wednesday, February 3, 2021 12:54 PM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] Re: #96 Toxtree will not open Kim, from your screenshot it's evident the ZIP got extracted to Toxtree-v3.1.0.1851 (2)....
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Kim, from your screenshot it's evident the ZIP got extracted to Toxtree-v3.1.0.1851 (2). So, instead of cd Toxtree-v3.1.0.1851, do cd "Toxtree-v3.1.0.1851 (2)" (make sure to put the quotation marks) and then continue with the video.
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Hi Luchesar, I followed the instructions and the video. I thought they were clear until I got command prompt error message. Please see screenshot below. Thanks. Kim [cid:image001.jpg@01D6FA0D.F4811F30] From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Tuesday, February 2, 2021 8:37 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] #96 Toxtree will not open Hi Kim, Thank you! It seems that you've deviated from the instructions, but I also understand...
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Hi Kim, Thank you! It seems that you've deviated from the instructions, but I also understand that they might've not been completely clear too. Here's a very basic video I've made with the steps: https://youtu.be/hn_kVGaTx00 Please download again Toxtree-v3.1.0.1851.zip from here and save or copy it to your desktop (that's very important: make sure to have the ZIP file on your desktop). Then right click the Toxtree-v3.1.0.1851.zip icon on your desktop and follow the video. Let me know if that works...
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Hi Luchesar, Below is the screenshot. I have been using Toxtree for over 10 years and I come to rely on it as my go-to computational tool. I never had a problem with HP Window 7. Now I have Lenovo Windows 10. I appreciate any suggestion you may have for my company tech support. Thanks. Kim [cid:image001.jpg@01D6F934.FED18D50] From: Li, Kim Sent: Monday, February 1, 2021 4:18 PM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net; Luchesar ILIEV luchesar@users.sourceforge.net Subject: RE: [External]...
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How exactly it "did not work"? Please understand that without enough information from your side, it's all but impossible to guess what the problem might be.
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Hi Luchesar, I followed the instructions but it didn't work. I had our company tech support follow the same instructions and again it didn't work. Do you have other suggestions for our tech support? Thanks. Kim From: Luchesar ILIEV luchesar@users.sourceforge.net Sent: Saturday, January 30, 2021 6:43 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] Re: #96 Toxtree will not open Kim, 1) Download Toxtree-v3.1.0.1851.zip from herehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Ftoxtree%2Ffiles%2Ftoxtree%2FToxtree-v.3.1.0%2F&data=04%7C01%7Clik%40amgen.com%7C2405b079f9684c93fe8d08d8c52d5f64%7C4b4266a6136841afad5a59eb634f7ad8%7C0%7C0%7C637476146521623165%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=HpP868zKMVeJotNeyy1QlG8ZP%2FH%2FjE%2FEABJWEk7LQTM%3D&reserved=0....
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Program not opening despite latest Java SE runtime being installed on machine
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Original problem was successfully resolved. Later comments are related to #96. Closing.
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Kim, 1) Download Toxtree-v3.1.0.1851.zip from here. 2) Extract the ZIP archive in some directory/folder. 3) Open a command prompt in the directory/folder where you extracted the files. 4) Enter the Toxtree subdirectory (e.g. cd Toxtree). 5) Run javaw -jar Toxtree-3.1.0.1851.jar Cheers, Luchesar
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Hi Nina, I have files below. Are they the zip archive? If not, can you point me to where I can download the zip archive? How do I launch the command line from Windows 10? Thanks. Kim [cid:image001.jpg@01D6F620.21433F90] From: Nina Jeliazkova vedina@users.sourceforge.net Sent: Thursday, January 28, 2021 10:20 PM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: [External] [toxtree:bugs] #96 Toxtree will not open Please provide details have you tried downloading the zip archive (instead...
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Hi Nina, From the zip archive in my download, I extracted all files to the default location C drive. When I run the command line I have the following error message. Please help. Thanks. Kim [cid:image001.jpg@01D6F63D.2445F210] From: Li, Kim Sent: Friday, January 29, 2021 9:22 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net<mailto:96@bugs.toxtree.p.re.sourceforge.net> Subject: RE: [External] [toxtree:bugs] #96 Toxtree will not open Hi Nina, I have files below. Are they the zip archive?...
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Hi Nina, From the zip archive in my download, I extracted all files to the default location C drive. When I run the command line I have the following error message. Please help. Thanks. Kim [cid:image002.jpg@01D6F637.43D44FB0] From: Li, Kim Sent: Friday, January 29, 2021 9:22 AM To: [toxtree:bugs] 96@bugs.toxtree.p.re.sourceforge.net Subject: RE: [External] [toxtree:bugs] #96 Toxtree will not open Hi Nina, I have files below. Are they the zip archive? If not, can you point me to where I can download...
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Please provide details have you tried downloading the zip archive (instead of the installer) and launching via command line javaw -jar Toxtree-version.jar Please note the installer is NOT tested on Windows10 and may not work.
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Dear Kim LI, Could you please provide details - have you installed from zip archive or using the installer ? What are the messages when typing on command prompt javaw -jar Toxtree-verison.jar
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Toxtree will not open
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Program not opening. I had our company IT support check all requirements, even uninstalled and reinstalled with administrative privilege. We also tried the v2.6 for Windows 10. Nothing worked
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Raffaella Meffe created ticket #95
Kroes TTC decision tree
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Vinod Goyal posted a comment on discussion Open Discussion
Hi, I have downloaded the sodtware but unable of launch it. Tried several time without any success.
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I was using the Revised Cramer rules Oh, ok, we'll check the implementation. There is no manual for the RDT yet, but the descriptions of rules can be examined the same way as above. And of course the source code.
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Todd Kennedy posted a comment on ticket #94
Thank you for the response. I will refer to the manual and other references. I was using the Revised Cramer rules so Q22 is about the number of carbons in the rings of the structure. For the query structure above, the Toxtree answer appears to be incorrect. It answered "No" when there are many more ring carbons than 12.
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The question 1 (Normal constituent of the body) relies on predefined lookup list, so if this particular structure is not in the list, the answer will be "No". Returns true if the query is isomorphic to one of the structures loaded from a preconfigured file of a type SDF, SMI, CSV Is the substance a normal constituent of the body, or an optical isomer of such?This question throws into class I all normal constituents of body tissues and fluids, including normal metabolites. Hormones are excluded, as...
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The question 1 (Normal constituent of the body) relies on predefined lookup list, so if this particular structure is not in the list, the answer will be "No". Returns true if the query is isomorphic to one of the structures loaded from a preconfigured file of a type SDF, SMI, CSV Is the substance a normal constituent of the body, or an optical isomer of such?This question throws into class I all normal constituents of body tissues and fluids, including normal metabolites. Hormones are excluded, as...
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The question 1 (Normal constituent of the body) relies on predefined lookup list, so if this particular structure is not in the list, the answer will be "No". Returns true if the query is isomorphic to one of the structures loaded from a preconfigured file of a type SDF, SMI, CSV Is the substance a normal constituent of the body, or an optical isomer of such?This question throws into class I all normal constituents of body tissues and fluids, including normal metabolites. Hormones are excluded, as...
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Questions on Revised Cramer Rules for a bicyclo-diester compound
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Dana Ramanan posted a comment on ticket #93
Hi Nina, Thank you for following up with me! OS: Windows 10 Home, Version 1909, Build 18363.1016 JRE Version 8 Update 261 However, I noticed I didn't have JDK and was able to get it working after downloading the latest JDK version https://www.oracle.com/java/technologies/javase-downloads.html (Java SE 14.0.2). It works fine now! Dana On Thu, Aug 27, 2020 at 2:49 AM Nina Jeliazkova vedina@users.sourceforge.net wrote: Could you please provide more details : - operating system & version - JRE version...
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Could you please provide more details : - operating system & version - JRE version - are you trying to launch Toxtree through the installer ? Please note the Windows installer is not tested on Windows 10. An alternative option to using the Windows installer is to download the zip archive, unzip and try javaw -jar Toxtree-verison.jar from command line.
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Program not opening despite latest Java SE runtime being installed on machine
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fixed 3.1.0 download links
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4.0.0-SNAPSHOT version with ambit 4.0.1-SNAPSHOT
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changed as requested
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updating outdated SVN links to test files to the current git ones
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EDIONE CANZI posted a comment on ticket #90
Can someone help me with this problem?
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Unable to use CAS No. Search
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The remote server was down, should work now, Apologies for the inconvenience.
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Unable to use CAS No. Search
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Up unit late Friday June 14, 2019, I had no problem just typing in a CAS No. into the "Chemical id" line and getting information. Now it is taking forever to run and only comes back with a reply "CAS entered, failed to retrieve from remote server". I have tried queeries that have run before successfully and they are not currently getting any ToxTree information. The remote query option is selected. Is anyone else having an issue? Any suggestions? I have tried both the version 2.6.13 and the latest...
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zhen jiang posted a comment on discussion Open Discussion
who can told me the difference between Cramer and Cramer with extension. thx
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Is there any method generate a report about the estimation?
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cramer 3 serialization issues fixed
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Skin irritation Rule 4
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The rule name is wrong. The rules Q4, Q33,Q9, Q19 are verifying if the structure has only these elements, according to the rules published in Walker JD, Gerner I, Hulzebos E, Schlegel K: The Skin Irritation Corrosion Rules Estimation Tool (SICRET). QSAR Comb Sci 2005, 24:378–384. https://onlinelibrary.wiley.com/doi/pdf/10.1002/qsar.200430906 (table 1) This is fixed with commit https://sourceforge.net/p/toxtree/git/ci/c2b1b96ab8f43f8e1289f4ba8f4834838add3738/ and the correct naming will be included...
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Fixed wrong rule description https://sourceforge.net/p/toxtree/bugs/91/
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Skin irritation Rule 4
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Skin irritation Rule 4
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favicon
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smaller image
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FAQ updated
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Ames plugin QSAR not working
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files added and img resized
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site update with more recent maven skin
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Upgrade to cdk 2.x.x & ambit 4.x
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links to plugin source codes modified T368
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links to donations page
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Donations
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Toxtree branch with AMBIT 2.6.0-SNAPSHOT (CDK 1.5.3)
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Disable JCP for now
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Disable JCP for now
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updated to cdk 1.5.6-SNAPSHOT
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CDK dependency upgraded to 1.5.3
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Experimental Toxtree version with cdk 1.5-SNAPSHOT
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Toxtree branch refactored to compile with cdk 1.5
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bug 2030363 fix
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ISS plug-in for the in vivo micronucleus assay sources for ToxTree 1.5x
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rebuild jars for 1.51 (bug fixes)
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Fixed bug [ 2026989 ] Saving new decision tree doesn't work
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Implementation of feature request 2117623 (trunk and 1.50 branch)
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toxtree-1.50 release
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fixed null pointer bug (options panel not assigned)
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bug fix for 2031864
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version changed to 1.51
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Bug fix (on behalf of Olga Tcheremenskaia)
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Build 1.51.23092008
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fixed broken html
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HTML Java doc files removed, should be in a compressed format
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1.33 branch
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moving previous versions to branches
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helper dir copied to branch 1.40