jalview-manual.git
12 months agotodo for reinstating exercise on editing alignment parameters master
Jim Procter [Fri, 2 Oct 2020 16:54:03 +0000 (17:54 +0100)]
todo for reinstating exercise on editing alignment parameters

12 months agominor tweak wording
Jim Procter [Fri, 2 Oct 2020 16:53:35 +0000 (17:53 +0100)]
minor tweak wording

12 months agohttp to https
Jim Procter [Fri, 2 Oct 2020 16:53:11 +0000 (17:53 +0100)]
http to https

12 months agofix up ‘enabling group consensus’ in column-based subgroup conservation analysis...
Jim Procter [Fri, 2 Oct 2020 16:27:09 +0000 (17:27 +0100)]
fix up ‘enabling group consensus’ in column-based subgroup conservation analysis exercise and mention ‘recommended column’ for creating subgroups

12 months agoClarify instructions on how to insert gaps with the mouse
Jim Procter [Fri, 2 Oct 2020 16:25:49 +0000 (17:25 +0100)]
Clarify instructions on how to insert gaps with the mouse

12 months agoexplaining in more detail about disabling feature colours if they are shown in the...
Jim Procter [Fri, 2 Oct 2020 16:15:14 +0000 (17:15 +0100)]
explaining in more detail about disabling feature colours if they are shown in the colouring alignments exercise

12 months agominor rewording/style fixing
Jim Procter [Fri, 2 Oct 2020 16:14:17 +0000 (17:14 +0100)]
minor rewording/style fixing

12 months agoremind people to look at next page for exercises, and note about ‘homework exercises...
Jim Procter [Fri, 2 Oct 2020 16:08:32 +0000 (17:08 +0100)]
remind people to look at next page for exercises, and note about ‘homework exercises’ 7 and 8 for course participants

12 months agospell out path to menu items in hide/show exercise
Jim Procter [Fri, 2 Oct 2020 16:07:32 +0000 (17:07 +0100)]
spell out path to menu items in hide/show exercise

12 months agoctrl/CMD for toggling sequences in creating groups exercise (the use of shift is...
Jim Procter [Fri, 2 Oct 2020 16:06:50 +0000 (17:06 +0100)]
ctrl/CMD for toggling sequences in creating groups exercise (the use of shift is demonstrated in another of the exercise’s steps)

12 months agocomment to slduce about section about jalview projects widowed at end of chapter.
Jim Procter [Fri, 2 Oct 2020 16:04:35 +0000 (17:04 +0100)]
comment to slduce about section about jalview projects widowed at end of chapter.

12 months agotweaked jalview projects section
Jim Procter [Fri, 2 Oct 2020 16:03:52 +0000 (17:03 +0100)]
tweaked jalview projects section

12 months agoRevised exercise 1 - launching Jalview in line with 2.11.1.2 changes
Jim Procter [Fri, 2 Oct 2020 16:03:13 +0000 (17:03 +0100)]
Revised exercise 1 - launching Jalview in line with 2.11.1.2 changes

12 months agoRevised intro about launching Jalview and removed commented out JNLP stuff
Jim Procter [Fri, 2 Oct 2020 16:02:30 +0000 (17:02 +0100)]
Revised intro about launching Jalview and removed commented out JNLP stuff

12 months agoignore eclipse project metadata directory
Jim Procter [Wed, 30 Sep 2020 13:34:52 +0000 (14:34 +0100)]
ignore eclipse project metadata directory

12 months agoJust notice an extra space introduced in error. So corrected it and have
sduce [Fri, 25 Sep 2020 15:17:09 +0000 (16:17 +0100)]
Just notice an extra space introduced in error. So corrected it and have
submitted this fourth commit. That me done for now.

12 months agoI have updated the Figure 1.2 (download) and 1.3 (splash screen).
sduce [Fri, 25 Sep 2020 15:11:37 +0000 (16:11 +0100)]
I have updated the Figure 1.2 (download) and 1.3 (splash screen).

12 months agoUpdated the exercise and related text about launching Jalview. Also
sduce [Fri, 25 Sep 2020 14:40:23 +0000 (15:40 +0100)]
Updated the exercise and related text about launching Jalview. Also
rearranged text so chapter 1 didnt have lots of white space due to
latex's format issues.
Also corrected some typos.

12 months agoUpdated manual after testing Jalview develop
sduce [Fri, 25 Sep 2020 10:02:42 +0000 (11:02 +0100)]
Updated manual after testing Jalview develop

12 months agoUpdated the manual after testing jalview develop
sduce [Fri, 25 Sep 2020 09:35:55 +0000 (10:35 +0100)]
Updated the manual after testing jalview develop

2 years agoI have read through the text and gone through the exercises (up to
Suzanne Duce [Fri, 10 May 2019 14:48:58 +0000 (15:48 +0100)]
I have read through the text and gone through the exercises (up to
Chapter 9) and updated as appropriate.

2 years agoJAL-3111 TODOs for next workshop/revision
Jim Procter [Wed, 8 May 2019 14:37:36 +0000 (15:37 +0100)]
JAL-3111 TODOs for next workshop/revision

2 years agoJAL-3111 clarify exercise step in sub-family covariation analysis
Jim Procter [Wed, 8 May 2019 14:36:30 +0000 (15:36 +0100)]
JAL-3111 clarify exercise step in sub-family covariation analysis

2 years agoJAL-3111 patch exercises for revised Structure Viewer dialog
Jim Procter [Wed, 8 May 2019 14:35:21 +0000 (15:35 +0100)]
JAL-3111 patch exercises for revised Structure Viewer dialog

2 years agoversion 1.9.2 Version_1.9.2
Jim Procter [Fri, 26 Apr 2019 13:46:16 +0000 (14:46 +0100)]
version 1.9.2

2 years agomany image updates and also tweaks for 2.11 release
Jim Procter [Fri, 26 Apr 2019 13:40:51 +0000 (14:40 +0100)]
many image updates and also tweaks for 2.11 release

2 years agoUpdated .project and .gitignore after import to eclipse
Jim Procter [Wed, 17 Apr 2019 16:51:11 +0000 (17:51 +0100)]
Updated .project and .gitignore after import to eclipse

2 years agorename eclipse project
Jim Procter [Wed, 17 Apr 2019 16:39:11 +0000 (17:39 +0100)]
rename eclipse project

2 years agoupdate gitignore
Jim Procter [Wed, 17 Apr 2019 16:36:44 +0000 (17:36 +0100)]
update gitignore

3 years agoTwo issues were reported during the Jalview workshop day so I fixed them.
Suzanne Duce [Fri, 24 Nov 2017 13:27:05 +0000 (13:27 +0000)]
Two issues were reported  during the Jalview workshop day so  I fixed them.

3 years agominor tweaks after proofing prior to 17th November 2017 course
Jim Procter [Tue, 21 Nov 2017 16:42:45 +0000 (16:42 +0000)]
minor tweaks after proofing prior to 17th November 2017 course

3 years agoJust spooted a slight format issue
Suzanne Duce [Fri, 17 Nov 2017 15:56:50 +0000 (15:56 +0000)]
Just spooted a slight format issue

3 years agoThis is the third manual commit. I checked the exercise again and made a few addition...
Suzanne Duce [Fri, 17 Nov 2017 15:42:06 +0000 (15:42 +0000)]
This is the third manual commit. I checked the exercise again and made a few additional changes. It is now ready to send to the printers.

3 years agoModified some of the exercises esp the tree and pca exercises. Plus corrected a few...
Suzanne Duce [Thu, 16 Nov 2017 11:56:37 +0000 (11:56 +0000)]
Modified some of the exercises esp the tree and pca exercises. Plus corrected a few typos.

3 years agoI am committing the edits to the main body of the text. I will work on the exercises...
Suzanne Duce [Fri, 10 Nov 2017 15:29:06 +0000 (15:29 +0000)]
I am committing the edits to the main body of the text. I will work on the exercises next.

4 years agoversion 1.9 of jalview manual
Jim Procter [Mon, 20 Feb 2017 16:03:47 +0000 (16:03 +0000)]
version 1.9 of jalview manual

4 years agoupdate version to 1.9, and date to today.
Jim Procter [Mon, 20 Feb 2017 15:56:04 +0000 (15:56 +0000)]
update version to 1.9, and date to today.

4 years agoUpdated info on PCA calculation (SeqSpace vs BLOSUM62)
Jim Procter [Mon, 20 Feb 2017 13:32:22 +0000 (13:32 +0000)]
Updated info on PCA calculation (SeqSpace vs BLOSUM62)
Structures - new Structure Chooser figure, simplified descriptions in text.
EMBL->ENA

4 years agominor rewording, typo fixes, and more complete introduction to the Jalview/UCSF Chime...
Jim Procter [Sun, 19 Feb 2017 17:59:06 +0000 (17:59 +0000)]
minor rewording, typo fixes, and more complete introduction to the Jalview/UCSF Chimera relationship.

4 years agoMade changes to improve layout of manual
Suzanne Duce [Wed, 15 Feb 2017 17:41:55 +0000 (17:41 +0000)]
Made changes to improve layout of manual

4 years agoChanged JNet to JPred in manual
Suzanne Duce [Wed, 15 Feb 2017 17:16:35 +0000 (17:16 +0000)]
Changed JNet to JPred  in manual

4 years agoCorrect a few typos.
Suzanne Duce [Fri, 3 Feb 2017 15:58:48 +0000 (15:58 +0000)]
Correct a few typos.

4 years agoUpdated the some of the images in the manual
Suzanne Duce [Wed, 14 Dec 2016 15:46:12 +0000 (15:46 +0000)]
Updated the some of the images in the manual

5 years agodropped out some sections for Glasgow 2016, and quick rework of View 3D Structure...
Jim Procter [Wed, 12 Oct 2016 15:35:28 +0000 (15:35 +0000)]
dropped out some sections for Glasgow 2016, and quick rework of View 3D Structure instructions.

5 years agoMore exercise tweaks - regularise warnings/platform help, some typos, and reinstated...
Jim Procter [Wed, 12 Oct 2016 13:48:02 +0000 (13:48 +0000)]
More exercise tweaks - regularise warnings/platform help, some typos, and reinstated the three-domain pfam alignment/protein-dna structure exercise.
fixed subsection hierarchy, added blurb and tweaked names of chapters...

5 years agohints should always be placed on a new line in the exercise.
Jim Procter [Tue, 11 Oct 2016 11:36:18 +0000 (11:36 +0000)]
hints should always be placed on a new line in the exercise.
also add link between the annotation and jpred exercises for the 'homework'

5 years agotweak formating before editing exercises.
Jim Procter [Tue, 11 Oct 2016 11:20:31 +0000 (11:20 +0000)]
tweak formating before editing exercises.
note about JAL-2118 (new row is sorted when interacted with)

5 years agoreplaced all instances of 'dialogue' with 'dialog'.
Jim Procter [Tue, 11 Oct 2016 09:26:56 +0000 (09:26 +0000)]
replaced all instances of 'dialogue' with 'dialog'.
shortened 'a video about this exercise' to 'See the video at' for all exercises.
fixed database fetcher exercise.
moved undoing edits to top of 'introducing gaps' section, reordered exercises.
tidied up for Kira's comments up to end chapter 3.
Tidied up chapter 3 summary.

5 years agocrop to make close all figure (sec 1.3 after Fig 1.7) more visible
Jim Procter [Mon, 10 Oct 2016 14:13:48 +0000 (14:13 +0000)]
crop to make close all figure (sec 1.3 after Fig 1.7) more visible

5 years agoI have implemented more of Kira's suggestions. Some of the exercises need more time...
Suzanne Duce [Fri, 7 Oct 2016 15:59:37 +0000 (15:59 +0000)]
I have implemented more of Kira's suggestions. Some of the exercises need more time to do properly. Will return to them.

5 years agoI have changed the manual in light of Kira's comments.
Suzanne Duce [Fri, 7 Oct 2016 13:42:18 +0000 (13:42 +0000)]
I have changed the manual in light of Kira's comments.
I have got to page 71 so far.

I haven't changed any figures.

5 years agoJust updating the date on the manual
Suzanne Duce [Wed, 28 Sep 2016 15:52:36 +0000 (15:52 +0000)]
Just updating the date on the manual

5 years agoI have proof read manual after yesterday edits and have few more corrects to layout.
Suzanne Duce [Fri, 16 Sep 2016 16:11:14 +0000 (16:11 +0000)]
I have proof read manual after yesterday edits and have few more corrects to layout.
Again there is something wrong with document and its generating errors but I can still generate a pdf.

5 years agoI am committing this edits even though there are some errors message.
Suzanne Duce [Thu, 15 Sep 2016 16:16:54 +0000 (16:16 +0000)]
I am committing this edits even though there are some errors message.
I think the errors are due to lost pdf links.
I hope to sort this out when Jim is in next.

5 years ago(A) Polishing the exercises that I have recently created videos for.
Suzanne Duce [Thu, 1 Sep 2016 16:21:40 +0000 (16:21 +0000)]
(A) Polishing the exercises that I have recently created videos for.
(B) Creating 2 new exercises. The first was to divide an existing exercise. The second was to add exercise to open chimera.

5 years agoChanged pca exercise.
Suzanne Duce [Thu, 9 Jun 2016 11:57:09 +0000 (11:57 +0000)]
Changed pca exercise.
Also tidied up the appearance a little.

5 years agoI have correct principle/principal typos in four locations in PCA section.
Suzanne Duce [Thu, 9 Jun 2016 09:22:03 +0000 (09:22 +0000)]
I have correct principle/principal typos in four locations in PCA section.

5 years agoChange wording in MSA section about ordering sequences
Suzanne Duce [Fri, 13 May 2016 13:24:36 +0000 (13:24 +0000)]
Change wording in MSA section about ordering sequences

5 years agoAdded annotation sections and made few minor changes.
Suzanne Duce [Fri, 13 May 2016 09:10:41 +0000 (09:10 +0000)]
Added annotation sections and made few minor changes.

5 years agoChanges for Feb 2016 SLS course
Suzanne Duce [Thu, 18 Feb 2016 16:48:07 +0000 (16:48 +0000)]
Changes for Feb 2016 SLS course

6 years agoI have gone through all the exercises in the manual checking them and making changes...
Suzanne Duce [Fri, 1 May 2015 15:49:43 +0000 (15:49 +0000)]
I have gone through all the exercises in the manual checking them and making changes as appropriate. Most things worked fine but JPred wasnÕt working. I modified the RNA exercise in light of database changes and this is now useable. Some of the images seem to disappeared -might be worth double checking. So Jim I pass the baton onto you.

6 years agothursday edits to manual
Suzanne Duce [Thu, 30 Apr 2015 16:53:54 +0000 (16:53 +0000)]
thursday edits to manual

6 years agoReading the pdf I noticed an error in my edits for one of the exercises so corrected it.
Suzanne Duce [Fri, 24 Apr 2015 14:27:27 +0000 (14:27 +0000)]
Reading the pdf I noticed an error in my edits for one of the exercises so corrected it.

Plus I was not sure that I had correctly synced the last lot of correction in team, so i did that this time.

6 years agoI have added my corrections to chapter 1.
Suzanne Duce [Fri, 24 Apr 2015 14:10:07 +0000 (14:10 +0000)]
I have added my corrections to chapter 1.
I have 2 other comments
(i) we could update figure 1.1 about Jalview capabilities, as we have a version with Ô3DÕ coloured circles
(ii) In navigation mode section 1.3, it may be helpful to add some text about context sensitive pop up menus. Then users will know them before they met them in an exercise.

6 years agoChanges added after the London 2014 workshop
Suzanne Duce [Fri, 24 Apr 2015 11:16:22 +0000 (11:16 +0000)]
Changes added after the London 2014 workshop

6 years agoAdded Mungo's edits and standardised layout
Suzanne Duce [Fri, 19 Dec 2014 13:42:30 +0000 (13:42 +0000)]
Added Mungo's edits and standardised layout

6 years agoupdate version/date
Jim Procter [Fri, 12 Dec 2014 13:28:22 +0000 (13:28 +0000)]
update version/date

6 years agocommented out defunct exercises, added others, tweaked some language.
Jim Procter [Fri, 12 Dec 2014 09:12:09 +0000 (09:12 +0000)]
commented out defunct exercises, added others, tweaked some language.

6 years agonew figures for RNA section
Jim Procter [Fri, 12 Dec 2014 09:11:00 +0000 (09:11 +0000)]
new figures for RNA section

6 years agoSLD has completed her text and exercise edits in Chapter 1.
Suzanne Duce [Sat, 6 Dec 2014 12:43:43 +0000 (12:43 +0000)]
SLD has completed her text and exercise edits in Chapter 1.

6 years ago90% of chapter 1 edits for London workshop. Though I would like to test run the text...
Suzanne Duce [Fri, 5 Dec 2014 17:31:13 +0000 (17:31 +0000)]
90% of chapter 1 edits for London workshop. Though I would like to test run the text and exercises more if there was more time.

6 years agosecond commit (to test the process)
Suzanne Duce [Fri, 5 Dec 2014 16:30:10 +0000 (16:30 +0000)]
second commit (to test the process)

6 years agoUpdates for London 2014 workshop
Suzanne Duce [Fri, 5 Dec 2014 15:48:45 +0000 (15:48 +0000)]
Updates for London 2014 workshop

8 years agoincluded instructions to use ps2pdf to reduce the size of file generated by pdflatex...
Jim Procter [Sun, 7 Apr 2013 23:39:59 +0000 (23:39 +0000)]
included instructions to use ps2pdf to reduce the size of file generated by pdflatex, and to ensure that special symbols are preserved in the 'optimised for screen' version generated by Adobe Distiller.

8 years agov1.4.1 manual
Jim Procter [Fri, 1 Feb 2013 17:16:49 +0000 (17:16 +0000)]
v1.4.1 manual

8 years agoManual version 1.4.1 updated 18th January for Version 2.8 and EMBL-EBI course
Jim Procter [Fri, 1 Feb 2013 17:11:46 +0000 (17:11 +0000)]
Manual version 1.4.1 updated 18th January for Version 2.8 and EMBL-EBI course

8 years agov2.8 new website and logo
Jim Procter [Fri, 1 Feb 2013 17:10:21 +0000 (17:10 +0000)]
v2.8 new website and logo

8 years agov 2.8 logo and new top level help page
Jim Procter [Fri, 1 Feb 2013 17:10:10 +0000 (17:10 +0000)]
v 2.8 logo and new top level help page

8 years agov 2.8 logo and authors
Jim Procter [Fri, 1 Feb 2013 17:09:55 +0000 (17:09 +0000)]
v 2.8 logo and authors

8 years agov 2.8 capabilitis
Jim Procter [Fri, 1 Feb 2013 17:09:38 +0000 (17:09 +0000)]
v 2.8 capabilitis

8 years agov2.8 new database selector for sequence fetcher
Jim Procter [Fri, 1 Feb 2013 17:09:23 +0000 (17:09 +0000)]
v2.8 new database selector for sequence fetcher

8 years ago2.8 per sequence annotation colouring
Jim Procter [Fri, 1 Feb 2013 17:09:04 +0000 (17:09 +0000)]
2.8 per sequence annotation colouring

8 years ago2.8 colourschemes
Jim Procter [Fri, 1 Feb 2013 17:08:51 +0000 (17:08 +0000)]
2.8 colourschemes

8 years agorevised pca in v2.8
Jim Procter [Fri, 1 Feb 2013 17:08:20 +0000 (17:08 +0000)]
revised pca in v2.8

8 years agoalignment services in v2.8
Jim Procter [Fri, 1 Feb 2013 17:07:52 +0000 (17:07 +0000)]
alignment services in v2.8

8 years agov2.8 jabaws config with server status
Jim Procter [Fri, 1 Feb 2013 17:07:30 +0000 (17:07 +0000)]
v2.8 jabaws config with server status

8 years agov2.8 ws menu
Jim Procter [Fri, 1 Feb 2013 17:07:02 +0000 (17:07 +0000)]
v2.8 ws menu

8 years agov2.8 sequence disorder
Jim Procter [Fri, 1 Feb 2013 17:06:44 +0000 (17:06 +0000)]
v2.8 sequence disorder

8 years agov2.8 sequence details window
Jim Procter [Fri, 1 Feb 2013 17:06:11 +0000 (17:06 +0000)]
v2.8 sequence details window

8 years agoignore intermediate files
Jim Procter [Fri, 1 Feb 2013 17:03:43 +0000 (17:03 +0000)]
ignore intermediate files

8 years agoupdated tutorial for Jalview 2.7 - includes contributions from Saif Shehata
Jim Procter [Thu, 10 Jan 2013 18:01:17 +0000 (18:01 +0000)]
updated tutorial for Jalview 2.7 - includes contributions from Saif Shehata
(changes were made in June 2012)

9 years agoupdate to 1.3.01
Jim Procter [Mon, 5 Dec 2011 10:35:09 +0000 (10:35 +0000)]
update to 1.3.01

9 years agofix left-right page numbering and incorrect menu item
Jim Procter [Mon, 5 Dec 2011 10:28:44 +0000 (10:28 +0000)]
fix left-right page numbering and incorrect menu item

9 years agoupdated screen optimized version
Jim Procter [Tue, 29 Nov 2011 07:29:41 +0000 (07:29 +0000)]
updated screen optimized version

9 years agoupdated master document with dna alignment tools table
Jim Procter [Tue, 29 Nov 2011 07:19:05 +0000 (07:19 +0000)]
updated master document with dna alignment tools table

9 years agocompleted table of jabaws alignment services useful for DNA
Jim Procter [Tue, 29 Nov 2011 07:17:01 +0000 (07:17 +0000)]
completed table of jabaws alignment services useful for DNA

9 years agojalview manual v1.3 - updated for v2.7 of Jalview with new material for structure...
Jim Procter [Mon, 28 Nov 2011 16:14:25 +0000 (16:14 +0000)]
jalview manual v1.3 - updated for v2.7 of Jalview with new material for structure superposition and JABA server config.

9 years agodrag and drop association of PDB structures
Jim Procter [Mon, 28 Nov 2011 16:10:52 +0000 (16:10 +0000)]
drag and drop association of PDB structures

9 years agocolour by .. submenu figure
Jim Procter [Mon, 28 Nov 2011 16:10:41 +0000 (16:10 +0000)]
colour by .. submenu figure

9 years agodnmt1_mouse complex domain alignment colouring example
Jim Procter [Mon, 28 Nov 2011 16:10:12 +0000 (16:10 +0000)]
dnmt1_mouse complex domain alignment colouring example