formatting

docs/database/data-sources/index.rst

@@ -10,5 +10,4 @@ Contents
     custom/index
     apis/index
     id-resolvers
-    versions
     data-licences

docs/database/data-sources/library/index.rst

@@ -84,4 +84,4 @@ HumanMine Specific sources
 * orphanet
 * protein-atlas
 
-See `HumanMine <http://www.humanmine.org>`_ for more information about these datasets. Look at HumanMine's `project.xml <https://github.com/intermine/humanmine/blob/master/project.xml>`_ for examples of how to use these sources.
+See `HumanMine <http://www.humanmine.org>`_ for more information about these datasets. Look at `HumanMine's project.xml <https://github.com/intermine/humanmine/blob/master/project.xml>`_ for examples of how to use these sources.

docs/database/performance/precomputing.rst

@@ -134,16 +134,24 @@ The LOG records three queries:
 2. the generated SQL query
 3. the optimised query <-- this is where you will see your precomputed tables used
 
+IQL
+~~~~~~~~
 
-.. topic:: IQL 
+.. code-block:: guess
 
 	2013-10-30 16:59:24 INFO                              sqllogger     - (VERBOSE) iql: SELECT DISTINCT a7_, a2_, a3_, a8_, a5_, a6_ FROM org.intermine.model.bio.Interaction AS a1_, org.intermine.model.bio.Gene AS a2_, org.intermine.model.bio.InteractionDetail AS a3_, org.intermine.model.bio.InteractionExperiment AS a4_, org.intermine.model.bio.InteractionTerm AS a5_, org.intermine.model.bio.Publication AS a6_, org.intermine.model.bio.Gene AS a7_, org.intermine.model.bio.InteractionTerm AS a8_ WHERE (a1_.gene2 CONTAINS a2_ AND a1_.details CONTAINS a3_ AND a3_.experiment CONTAINS a4_ AND a3_.relationshipType CONTAINS a5_ AND a4_.publication CONTAINS a6_ AND a1_.gene1 CONTAINS a7_ AND a4_.interactionDetectionMethods CONTAINS a8_ AND a7_.id IN ? AND a2_.id IN ?) ORDER BY a7_.symbol, a2_.symbol, a3_.name, a3_.role1, a3_.role2, a3_.type, a8_.name, a5_.name, a6_.pubMedId 1: [1007850] 2: [2848406]
 
-.. topic:: generated sql
+Generated SQL
+~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: guess
 
 	generated sql: SELECT DISTINCT a7_.id AS a7_id, a2_.id AS a2_id, a3_.id AS a3_id, a8_.id AS a8_id, a5_.id AS a5_id, a6_.id AS a6_id, a7_.symbol AS orderbyfield1, a2_.symbol AS orderbyfield2, a3_.name AS orderbyfield3, a3_.role1 AS orderbyfield4, a3_.role2 AS orderbyfield5, a3_.type AS orderbyfield6, a8_.name AS orderbyfield7, a5_.name AS orderbyfield8, a6_.pubMedId AS orderbyfield9 FROM Interaction AS a1_, Gene AS a2_, InteractionDetail AS a3_, InteractionExperiment AS a4_, InteractionTerm AS a5_, Publication AS a6_, Gene AS a7_, InteractionTerm AS a8_, InteractionDetectionMethodsInteractionExperiment AS indirect0 WHERE a1_.gene2Id = a2_.id AND a1_.id = a3_.interactionId AND a3_.experimentId = a4_.id AND a3_.relationshipTypeId = a5_.id AND a4_.publicationId = a6_.id AND a1_.gene1Id = a7_.id AND a4_.id = indirect0.InteractionExperiment AND indirect0.InteractionDetectionMethods = a8_.id AND a7_.id IN (1007850) AND a2_.id IN (2848406) ORDER BY a7_.symbol, a2_.symbol, a3_.name, a3_.role1, a3_.role2, a3_.type, a8_.name, a5_.name, a6_.pubMedId, a7_.id, a2_.id, a3_.id, a8_.id, a5_.id, a6_.id LIMIT 5000
 
-.. topic:: optimised sql
+Optimised sql
+~~~~~~~~~~~~~~~~
+
+.. code-block:: guess
 
 	optimised sql: SELECT DISTINCT P98.a1_id AS a7_id, P98.a3_id AS a2_id, P96.id AS a3_id, a8_.id AS a8_id, a5_.id AS a5_id, a6_.id AS a6_id, P98.a1_symbol AS orderbyfield1, P98.a3_symbol AS orderbyfield2, P96.name AS orderbyfield3, P96.role1 AS orderbyfield4, P96.role2 AS orderbyfield5, P96.type AS orderbyfield6, a8_.name AS orderbyfield7, a5_.name AS orderbyfield8, a6_.pubMedId AS orderbyfield9 FROM precomp_45503 AS P98, InteractionDetail AS P96, InteractionExperiment AS P97, InteractionTerm AS a5_, Publication AS a6_, InteractionTerm AS a8_, InteractionDetectionMethodsInteractionExperiment AS indirect0 WHERE P98.a2_id = P96.interactionId AND P96.experimentId = P97.id AND P96.relationshipTypeId = a5_.id AND P97.publicationId = a6_.id AND P97.id = indirect0.InteractionExperiment AND indirect0.InteractionDetectionMethods = a8_.id AND P98.a1_id IN (1007850) AND P98.a3_id IN (2848406) ORDER BY P98.a1_symbol, P98.a3_symbol, P96.name, P96.role1, P96.role2, P96.type, a8_.name, a5_.name, a6_.pubMedId, P98.a1_id, P98.a3_id, P96.id, a8_.id, a5_.id, a6_.id LIMIT 5000
 

docs/get-started/index.rst

@@ -10,4 +10,3 @@ Get started
    create-your-mine
    testmine
    intermine-tests
-   amazon

docs/get-started/tutorial/index.rst

@@ -108,7 +108,11 @@ Specific operations can be performed on the Mine once data is loaded, these are
 Data to load
 ~~~~~~~~~~~~~~~
 
-The biotestmine git repository includes a tar file with data to load into BiotestMine. These are real, complete data sets for *P. falciparum* (but very old!). We will load genome annotation from PlasmoDB, protein data from UniProt and GO annotation also from PlasmoDB. See :doc:`/get-started/tutorial/test-data`for details on the data. 
+The biotestmine git repository includes a tar file with data to load into BiotestMine. These are real, complete data sets for *P. falciparum* (but very old!). 
+
+We will load genome annotation from PlasmoDB, protein data from UniProt and GO annotation also from PlasmoDB. 
+
+See :doc:`/get-started/tutorial/test-data`for details on the data. 
 
 Copy this to a local directory (your home directory is fine for this workshop) and extract the archive:
 
@@ -245,7 +249,7 @@ Sequence Ontology
     extraModelsEnd = ""
   }
 
-The first file merged into the core model is the `so_additions.xml` file.  This XML file is generated in the `dbmodel/build` directory from terms listed in the `so_terms` file, as configured in the `dbmodel/build.gradle <https://github.com/intermine/biotestmine/blob/master/dbmodel/build.gradle#L31>`_ file.
+The first file merged into the core model is the `so_additions.xml` file.  This XML file is generated in the `dbmodel/build` directory from terms listed in the `so_terms` file, as configured in the `dbmodel/build.gradle <https://github.com/intermine/biotestmine/blob/master/dbmodel/build.gradle#L31>`__ file.
 
 ::
 

docs/get-started/amazon.rst → docs/intermine/amazon.rst

@@ -24,22 +24,27 @@ The image contains a ready deployed MalariaMine.
 2. go to the EC2 management console
    AWS console https://console.aws.amazon.com/console/home --> EC2 console
 3. if you don't have one, set up a security group which allows access at least to port
+
   * 22 (SSH)
   * 80 (HTTP)
   * 8080 (TOMCAT)
+
   you could set up also a few spare ones (20, 21, 8009).
 
-  .. note::
+.. note::
+
    You can do this also during step 7, but **you cannot change the security group of an instance after starting it for the first time**
    (unless you use a VPC instance, see `User Guide <http://docs.aws.amazon.com/AmazonVPC/latest/UserGuide/VPC_Introduction.html>`_).
 
 4. go to the IMAGES/AMI console
 5. set the location on the top header (beside your username) to *US East (N. Virginia)*
-6. set the filter to *Public Images* and search for ``InterMine``
+6. set the filter to *Public Images* and search for **InterMine**
 7. select *BasicIntermine* AMI (AMI ID = ami-b1c7a9d8)
 8. launch (and configure) instance
+
   * you can use all default options for the instance characteristics and details, but use the security group you created in step 3.
   * when prompted, create a new key pair (``.pem`` file), or use one that you already own.
+
 9. go to the Instance console
 10. select your new instance
 11. when public DNS appears (after checks, a couple of minutes), you can open a terminal with

docs/intermine/index.rst

@@ -10,4 +10,5 @@ InterMine
    intermine-versions
    get-involved
    https
+   amazon
 

docs/intermine/upgrade.rst

@@ -22,7 +22,7 @@ To get patch updates automatically, use the plus (+) notation:
 	systemProp.imVersion=4.0.+
 	systemProp.bioVersion=4.0.+
 
-Read more: :doc:`</intermine/intermine-versions.rst>`_ and :doc:`</intermine/roadmap.rst>`_
+Read more: :doc:`</intermine/intermine-versions.rst>` and :doc:`</intermine/roadmap.rst>`
 
 InterMine 4.0.0
 ---------------------
@@ -92,8 +92,8 @@ InterMine 3.0.0
 
 This release adds Solr to InterMine. To upgrade, you will need to rebuild your database and install Solr.
 
- To Upgrade
- ~~~~~~~~~~~
+To Upgrade
+~~~~~~~~~~~
 
 1. Change your mine's `gradle.properties` file to `3.0.+`. If you have data sources, change the version they use too.
 
@@ -307,11 +307,6 @@ We are making some non-backwards compatible changes to our API. These three end
 Please update any code that references these end points.
 
 
-
----------------------------------
----------------------------------
----------------------------------
-
 Pre-InterMine 2.0 Upgrade Instructions
 ------------------------------------------------------------------
 
@@ -349,7 +344,6 @@ interaction viewer
 	The cytoscape tool uses the new model - will not work until you build a database with the new code
 
 Interactions
-^^^^^^^^^^^^^^
 
 +-------------------+-------------------------+-----------------------------+
 | class             | old                     | new                         |
@@ -370,7 +364,6 @@ Interactions
 +-------------------+-------------------------+-----------------------------+
 
 Protein Domains
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 +-------------------+-------------------+----------------------+
 | class             | old               | new                  |

docs/system-requirements/hardware/index.rst

@@ -40,10 +40,10 @@ OS
 * Use something mainstream and reliable like Linux or BSD
 * Use the system that your friendly sysadmin is most familiar with.
 * Not favourites:
+
  * Tru64
  * :doc:`solaris`
 
-
 What we use
 --------------------
 

docs/system-requirements/software/postgres/postgres.rst

@@ -108,7 +108,7 @@ PostgreSQL parameters
 
 For better performance. Read http://wiki.postgresql.org/wiki/Tuning_Your_PostgreSQL_Server for more information.
 
-.. htmlonly::
+
 ===============================   =============================
 Parameter                         Suggested value (build)
 ===============================   =============================

docs/web-services/index.rst

@@ -49,33 +49,33 @@ For information on the underlying API, and the supported libraries, please visit
 HTTP API
      Documentation on services available from mines: `<http://iodocs.apps.intermine.org>`_
 Java
-    `Download <https://github.com/intermine/intermine-ws-java>`_
-    | `API <http://intermine.org/intermine-ws-java/javadoc/>`_
-    | `Tutorial <https://github.com/intermine/intermine-ws-java-docs/>`_
-    | `Source <https://github.com/intermine/intermine-ws-java>`_
+    `Download <https://github.com/intermine/intermine-ws-java>`__
+    | `API <http://intermine.org/intermine-ws-java/javadoc/>`__
+    | `Tutorial <https://github.com/intermine/intermine-ws-java-docs/>`__
+    | `Source <https://github.com/intermine/intermine-ws-java>`__
 Perl Client
-    `Download | API <http://search.cpan.org/perldoc?Webservice%3A%3AInterMine>`_
-    | `Tutorial <https://metacpan.org/pod/distribution/Webservice-InterMine/lib/Webservice/InterMine/Cookbook.pod>`_ 
-    | `Source <https://github.com/intermine/intermine-ws-perl>`_
+    `Download | API <http://search.cpan.org/perldoc?Webservice%3A%3AInterMine>`__
+    | `Tutorial <https://metacpan.org/pod/distribution/Webservice-InterMine/lib/Webservice/InterMine/Cookbook.pod>`__ 
+    | `Source <https://github.com/intermine/intermine-ws-perl>`__
 Python Client
-    `Download <http://pypi.python.org/pypi/intermine>`_
-    | `API <http://intermine.org/intermine-ws-python>`_  
-    | `Tutorial <https://github.com/intermine/intermine-ws-python-docs/>`_ 
-    | `Source <https://github.com/intermine/intermine-ws-client.py>`_
+    `Download <http://pypi.python.org/pypi/intermine>`__
+    | `API <http://intermine.org/intermine-ws-python>`__  
+    | `Tutorial <https://github.com/intermine/intermine-ws-python-docs/>`__
+    | `Source <https://github.com/intermine/intermine-ws-client.py>`__
 Ruby Client
-    `Download | API <http://www.rubygems.org/gems/intermine>`_
+    `Download | API <http://www.rubygems.org/gems/intermine>`__
     | Tutorial 
-    | `Source <https://github.com/intermine/intermine-ws-ruby>`_
-JavaScript Client (for Browser and node.js)
-    `Download <https://npmjs.org/package/imjs>`_
-    | `API <http://alexkalderimis.github.io/imjs/>`_
+    | `Source <https://github.com/intermine/intermine-ws-ruby>`__
+JavaScript Client (for Bowser and node.js)
+    `Download <https://npmjs.org/package/imjs>`__
+    | `API <http://alexkalderimis.github.io/imjs/>`__
     | Tutorial
-    | `Source <https://github.com/intermine/imjs>`_
+    | `Source <https://github.com/intermine/imjs>`__
 R Client
-    `Download <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`_
-    | `Docs <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`_
-    | `Tutorial <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`_
-    | `Source <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`_
+    `Download <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`__
+    | `Docs <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`__
+    | `Tutorial <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`__
+    | `Source <http://bioconductor.org/packages/release/bioc/html/InterMineR.html>`__
 
 
 Authentication

docs/webapp/third-party-tools/jbrowse.rst

@@ -77,7 +77,7 @@ Add your new mine-based dataset to your configuration file. For example to add *
 Once in place, you can visit your JBrowse `index.html` and see the data from FlyMine_.
 
 Configuring InterMine's JBrowse integration
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 By default, all InterMine classes that inherit from the SequenceFeature model class will have tracks.