Additional student guidance

.gitignore

@@ -70,6 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+_build/
 
 # PyBuilder
 target/

README.md

@@ -8,6 +8,11 @@ This handbook uses [Jupyter Book](http://jupyterbook.org/).
 
 The current live version of this book can be found [here](https://jean-golding-institute.github.io/ask-jgi-handbook/pages/intro.html).
 
+## Quickstart 
+
+* Install dependencies: `pip install -r requirements.txt`
+* Build book: `jupyter-book build .`
+
 ## Contributors ✨
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

_config.yml

@@ -10,10 +10,18 @@ logo: images/logo.png
 execute:
   execute_notebooks: force
 
+exclude_patterns:
+- venv/*
+
 # Define the name of the latex output file for PDF builds
 latex:
   latex_documents:
     targetname: book.tex
+  latex_engine: pdflatex
+
+sphinx:
+  config:
+    language: en
 
 # Add a bibtex file so that we can create citations
 bibtex_bibfiles:

_toc.yml

@@ -24,8 +24,6 @@ parts:
     - file: pages/procedures/ticket-updates
     - file: pages/procedures/update-tracker
   - file: pages/procedures/meetings
-    sections:
-    - file: pages/procedures/indico
 - caption: Resources
   chapters:
   - file: pages/resources/other-services

pages/managers/access.md

@@ -2,83 +2,29 @@
 # Communications and Access
 
 New Ask-JGI team members will require the following:
-- Ask-JGI Slack channel [access](slack_access).
-- Ask-JGI mailbox [access](mailbox_access)
-- Ask-JGI tracker [access](filler)
-- Ask-JGI Weekly Meeting agenda [access](indico_access)
-
+- Ask-JGI Slack channel [access](slack_access)
+- Ask-JGI Shared mailbox [access](mailbox_access)
+- Ask-JGI SharePoint and Tracker [access](sharepoint_access)
 
 (slack_access)=
 ## Managing access on Slack
 
 All new students should register for the Bristol Data Science Slack
-Workspace. They will then need to be added to the ask-jgi channel.
+Workspace.
+
+They will then need to be added to the `#ask-jgi` channel.
 
 (mailbox_access)=
 ## Mailbox access
 
-All new students will need access to the Ask-JGI mailbox. 
+All new students will need access to the Ask-JGI mailbox.
 
-Access to shared mailboxes can be managed via the IT Services [shared
-mailboxes admin tool](https://www.bristol.ac.uk/it-services/applications/shared-mailboxes/sharedmailboxes)
-as described in these [instructions for requesting and managing shared
-mailboxes](https://uob.sharepoint.com/sites/systemsupport/SitePages/online-shared-mailbox-admin.aspx). 
+Access is managed via the IT Services [shared mailboxes admin tool](https://www.bristol.ac.uk/it-services/applications/shared-mailboxes/sharedmailboxes) as described in these [instructions for requesting and managing shared mailboxes](https://uob.sharepoint.com/sites/systemsupport/SitePages/online-shared-mailbox-admin.aspx).
 Ask-JGI mailbox access can be managed directly through [this link](https://www.bristol.ac.uk/it-services/applications/shared-mailboxes/sharedmailbox/MDAwNDk4NTY).
 
+(sharepoint_access)=
+## SharePoint and Tracker access
 
-(tracker_access)=
-## Tracker access
-
-In order to gain access to the Ask-JGI tracker, new students will need
-to be added to the group `grp-Jean Golding Institute AskJGI PhD
-Students`. 
-
-Access is managed
-[here](https://uob.sharepoint.com/teams/grp-jeangoldinginstituteteam/_layouts/15/people.aspx?MembershipGroupId=1001),
-and any existing JGI team member should be able to add a new member to
-this group.
-
-
-(indico_access)=
-## Managing access on indico
-
-Ask-JGI weekly meeting agendas are hosted on [indico](https://indico.cern.ch/). 
-Information about the JGI indico setup can be found [here](indico).
-
-When a new member joins the Ask-JGI team, one of the JGI indico
-managers will need to add the new member's indico account to the
-access list for the `Group Meetings` [indico
-category](https://indico.cern.ch/category/14729/). This can be done by
-someone with manage access to the JGI indico. 
-
-Follow the instructions below to add a new member to
-the `Group Meetings` indico category:
+In order to gain access to the Ask-JGI SharePoint and Tracker, new students will need to be added to the group `grp-Jean Golding Institute AskJGI PhD Students`.
 
-1.  Navigate to the Jean Golding Institute Group Meetings [indico
-   category](https://indico.cern.ch/category/14729/) and select the
-   `Manage category` icon, as shown in the image below. This will
-   direct you to the management area of the `Group Meetings` indico category.
-    ![indico manage category icon
-   screenshot](../../images/indico/indico_manage.jpg)
-    </br></br>
-2.  Once you have switched to the management area, select `Protection`
-   on the left hand navigation menu. This will take you to the
-   category protection settings. You will be able to see the list of
-   users who currently have access (the usernames and emails are
-   redacted in the image below). Select the option to add a user by
-   clicking the `User` icon at the
-   bottom of the list of existing users.
-    ![indico protection settings
-   screenshot](../../images/indico/indico_protection.jpg)
-    </br></br>
-3.  Selecting the add user option will open a window like that shown
-    in the image below. Here you should be able to search for the
-    member that you want to grant access to. Note that the user will
-    need to have already registered for an indico account in order for
-    this to work. 
-    ![indico set user access
-   screenshot](../../images/indico/indico_select_users.png)
-    </br></br>
-4.  Don't forget to save your changes. You should then be able to see
-    the new member listed in the access list, and they should be able
-    to access the group meeting agendas when they are signed in to indico.
+Access is managed [here](https://uob.sharepoint.com/teams/grp-jeangoldinginstituteteam/_layouts/15/people.aspx?MembershipGroupId=1001), and any existing JGI team member should be able to add a new member to this group.

pages/managers/contracts.md

@@ -22,11 +22,9 @@ downloaded and completed by the candidate and the Ask-JGI manager. The form must
 be sent to TSS at [email protected] **at least 3 weeks** prior to
 the commencement of Ask-JGI activities.
 
-
 To claim payment each month, students will need to send a completed
 time sheet to the JGI Manager, who will enter their hours on MyERP.
 
-
 There are some cases where the above criteria do not apply (see below subsections).
 
 #### Student already employed through UoB HR

pages/procedures/arranging-meetings.md

@@ -1,4 +1,4 @@
-(arranging-meetings)+
+(arranging-meetings)=
 # Arranging meetings
 
 It is common to receive queries in the mailbox that require a short
@@ -17,51 +17,48 @@ If meeting with the querier seems to be the most productive next
 step, reply to their email (including the tracking identification
 number) and suggest some times that you are able to meet. 
 
-- If you use
-  your university Outlook calendar, you can either suggest that they
-  book a meeting directly into your calendar at a time convenient for
-  them. For example:
-  ```
-  Dear XXX, 
-
-  Many thanks for geting in contact with Ask-JGI. Would it be useful
-  to have an introductory Teams call (30 minutes, say) to go over your
-  query in a little more detail and see how we might be able to
-  support? 
-  I can also explain how we might go about assisting and work out
-  which of our team would be best placed to help you.
-
-  I’ve cc’d my email address into this email – if you can get access to
-  my calendar then I’m happy for you to schedule something at a time that
-  suits you.
-
-  Kind regards,
-  XXX
-  {AskJGI-XXX}
-  ```
+- If you use your university Outlook calendar, you can either suggest that they book a meeting directly into your calendar at a time convenient for them.
+  For example:
 
-- or, you can ask permission to book a meeting in their calendar at
-  a time where their calendar shows them as being free.
+  > Dear XXX, 
+  > 
+  > Many thanks for getting in contact with Ask-JGI. Would it be useful
+  > to have an introductory Teams call (30 minutes, say) to go over your
+  > query in a little more detail and see how we might be able to
+  > support? 
+  > 
+  > I can also explain how we might go about assisting and work out
+  > which of our team would be best placed to help you.
+  > 
+  > I’ve cc’d my email address into this email – if you can get access to
+  > my calendar then I’m happy for you to schedule something at a time that
+  > suits you.
+  > 
+  > Kind regards,
+  > XXX
+  > {AskJGI-XXX}
+
+- or, you can ask permission to book a meeting in their calendar at a time where their calendar shows them as being free.
   For example:
-  ```
-  Dear XXX, 
-
-  Many thanks for geting in contact with Ask-JGI. Would it be useful
-  to have an introductory Teams call (30 minutes, say) to go over your
-  query in a little more detail and see how we might be able to
-  support? 
-  I can also explain how we might go about assisting and work out
-  which of our team would be best placed to help you.
-
-  If you'd like me to set up a meeting then please let me know. I
-  could do tomorrow afternoon or the following morning, for example?
-  Alternatively I can try to find a slot in your calendar if it is up
-  to date? 
 
-  Kind regards,
-  XXX
-  {AskJGI-XXX}
-  ```
+  > Dear XXX, 
+  > 
+  > Many thanks for getting in contact with Ask-JGI. Would it be useful
+  > to have an introductory Teams call (30 minutes, say) to go over your
+  > query in a little more detail and see how we might be able to
+  > support? 
+  > 
+  > I can also explain how we might go about assisting and work out
+  > which of our team would be best placed to help you.
+  > 
+  > If you'd like me to set up a meeting then please let me know. I
+  > could do tomorrow afternoon or the following morning, for example?
+  > Alternatively I can try to find a slot in your calendar if it is up
+  > to date? 
+  > 
+  > Kind regards,
+  > XXX
+  > {AskJGI-XXX}
 
 (meeting-followup)=
 ## Following up after a meeting
@@ -76,7 +73,7 @@ Sending summary emails are important:
 - It is helpful to repeat your key takeaways from the meetings to make
 sure that everyone attending the meeting has left on the same page.
 - Having a written record from the meeting is helpful for any future
-  follow-up with querier (particularly if the followup is handled by
+  follow-up with querier (particularly if the follow-up is handled by
   another team member).
 
 When composing your summary emails try to include the following:
@@ -107,6 +104,7 @@ Scientists will be happy to review any email before you send it.
 
 ```{note}
 Remember to update the Ask-JGI tracker after a meeting to reflect what has
-happened and what is expected to happen next (if any followup is expected). Update the status field to indicate whether the query is
+happened and what is expected to happen next (if any follow-up is expected). 
+Update the status field to indicate whether the query is
 resolved or still in progress.
 ```

pages/procedures/auto-replies.md

@@ -4,22 +4,20 @@
 When a new email is received in the Ask-JGI mailbox an automated
 response is generated, which looks something like:
 
-```
-Thank you for your Ask-JGI enquiry. Your query will be picked up by a member of the Ask-JGI team soon.
+> Thank you for your Ask-JGI enquiry. Your query will be picked up by a member of the Ask-JGI team soon.
+> 
+> In the meantime please reply to this email to provide any
+> supplementary information to your question. 
+> Make sure you include this phrase somewhere in the email:
+> {AskJGI-110}. 
+> This helps us to track how the AskJGI service is used.
+> 
+> Suggested additional information:
+>  1. Your research question
+>  2. Any relevant papers / draft manuscripts etc.
+>  3. A description of your data (and a sample if you can send it)
+>  4. Any relevant analysis scripts/code that you have produced so far.
 
-In the meantime please reply to this email to provide any
-supplementary information to your question. 
-Make sure you include this phrase somewhere in the email:
-{AskJGI-110}. 
-This helps us to track how the AskJGI service is used.
-
-Suggested additional information:
- 1. Your research question
- 2. Any relevant papers / draft manuscripts etc.
- 3. A description of your data (and a sample if you can send it)
- 4. Any relevant analysis scripts/code that you have produced so far.
-
-```
 It is important that, when you respond to the initial query, you
 either:
 - "reply all" to this automated reply from Ask-JGI, or

pages/procedures/getting-started.md

@@ -13,6 +13,7 @@ that you are able to access some platforms, pages and groups. Please
 see the sections below for instructions on how to get yourself ready
 for your first shift. 
 
+(communicating-slack)=
 ## Communicating on Slack
 
 The platform that the Ask-JGI team uses to stay in touch on a
@@ -26,19 +27,22 @@ Sign up to join the **Bristol Data Science Network** Slack Workspace
 [here](https://www.bristol.ac.uk/golding/get-involved/build-your-network/slack/).
 
 Once you have signed in you should ask the Ask-JGI coordinator to add
-you to the private ask-jgi channel, which is the channel that the team
+you to the private `#ask-jgi` channel, which is the channel that the team
 uses to communicate about all things Ask-JGI.
 
-## Getting set up with indico
+## Getting set up with SharePoint
+
+Ask-JGI students should request access to the 
+Ask-JGI SharePoint folder, which can be found [here](https://uob.sharepoint.com/:f:/r/teams/grp-jeangoldinginstituteteam/Shared%20Documents/Ask-JGI?csf=1&web=1&e=imr5IE).
+In this folder you will be able to access weekly-agendas 
+for meetings, and store files related to any of your queries.
 
 While working with Ask-JGI you will be expected to
-attend weekly catch up meetings with the rest of the team. 
+attend weekly catch-up meetings with the rest of the team. 
+The Ask-JGI weekly meetings are managed through the Ask-JGI
+[SharePoint](https://uob.sharepoint.com/:f:/r/teams/grp-jeangoldinginstituteteam/Shared%20Documents/Ask-JGI?csf=1&web=1&e=YS5XKF). 
 
-The Ask-JGI weekly meetings are managed through
-[indico](https://indico.cern.ch/). You will need to set up an account
-to be able to access Ask-JGI meeting agendas online. Please find
-information about indico [here](indico), and instructions on
-registering for an account [here](account).
+Login using your UoB account.
 
 ## Ask-JGI mailbox access