From tbooth at ceh.ac.uk Wed Sep 7 10:42:02 2011 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 07 Sep 2011 15:42:02 +0100 Subject: [Bio-Linux] Drawing biological pathways with PathVisio Message-ID: <1315406522.3828.13119.camel@barsukas> Hi All, I've just been trying out the PathVisio tool (www.pathvisio.org) for editing biological pathways, and thought it might be of interest to people on this list. I've not yet had a chance to add the package to Bio-Linux but this isn't a problem as it can be run in one click via Java Webstart - see: http://www.pathvisio.org/wiki/PathVisioDownload My usual tool of choice for editing graphics is Inkscape (inkscape.org, available on Bio-Linux via Synaptic). However, this is a big and complex tool and of course has no awareness of the meaning of biological pathways nor any pre-made pathway files to work with. PathVisio is much more suited to this specific task. I've been talking to one of the authors of PathVisio who said he would like to encourage its uptake by Bio-Linux users, and of course it is always useful (and gratifying) to hear that people are making use of the software, so if you have any comments please do share them on this list. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From C.Burns at warwick.ac.uk Tue Sep 20 06:28:36 2011 From: C.Burns at warwick.ac.uk (Burns, Caitlin) Date: Tue, 20 Sep 2011 11:28:36 +0100 Subject: [Bio-Linux] Editing custom_parameters on QIIME Message-ID: Hello, I'm having trouble editing my custom_parameters.txt folder in Qiime. It is a read-only file and states: you are not the owner, so you cannot change these permissions. The owner is root. I have tried to paste in an edited version of custom_parameters but it wont even allow me to add anything to the qiime tutorial folder. How do I get permission or change the settings? I am using Biolinux from a memory stick that was given to us by CEH Wallingford. Thanks, Caitlin Caitlin Burns PhD student School of Life Sciences University of Warwick Wellesbourne campus Warwickshire CV35 9EF -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Sep 20 11:48:04 2011 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 20 Sep 2011 16:48:04 +0100 Subject: [Bio-Linux] Sorry for the service interruption Message-ID: <1316533684.25579.11278.camel@barsukas> Hi All, Due to a technical problem on this mailing list server we seem to have a couple of weeks mailings backed up, which have only now been processed all at once. I'm told the problem is now resolved. I'll endeavour to keep a better eye out for problems like this but if you do spot any issues with this or any other of the NEBC web services please feel free to complain loudly to helpdesk at nebc.nerc.ac.uk. Due to the nature of the local network we occasionally have weekend outages but in general we try to fix problems promptly and to keep everything up and running full time. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tbooth at ceh.ac.uk Tue Sep 20 12:02:00 2011 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 20 Sep 2011 17:02:00 +0100 Subject: [Bio-Linux] Editing custom_parameters on QIIME In-Reply-To: References: Message-ID: <1316534520.25579.11320.camel@barsukas> Hi Caitlin, Sorry, this is not very obvious from the tutorial documentation. The idea is that you copy both the data and the custom_parameters.txt to a directory in your home folder. You will then be the owner of all the newly copied files and able to edit them. So, for example, to work on the tutorial data: Click "Introductory Tutorial" on the desktop Right click on "qiime_tutorial_data.tar.gz" Extract To... and now select your home folder (ie. /home/live) A "qiime_tutorial_data" folder will appear in your home directory If you want to work on some of your own data you normally just want to copy the default qiime_parameters.txt into the folder where your data is before customising it - eg: cp /usr/share/doc/qiime/qiime_parameters.txt ~/my_data_for_qiime/custom_parameters.txt Does that make sense? Cheers, TIM On Tue, 2011-09-20 at 11:28 +0100, Burns, Caitlin wrote: > Hello, > > I'm having trouble editing my custom_parameters.txt folder in Qiime. > It is a read-only file and states: you are not the owner, so you > cannot change these permissions. The owner is root. I have tried to > paste in an edited version of custom_parameters but it wont even allow > me to add anything to the qiime tutorial folder. > > How do I get permission or change the settings? I am using Biolinux > from a memory stick that was given to us by CEH Wallingford. > > Thanks, > > Caitlin > > > Caitlin Burns > > PhD student > > School of Life Sciences > University of Warwick > Wellesbourne campus > Warwickshire > CV35 9EF > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.