diff --git a/docs/protocols.md b/docs/protocols.md index af4e0ab5cfe93c8e90aed32b4a8db63adc1d4eb4..08fcb062d35df51a309d9826b0ca6420379b1246 100644 --- a/docs/protocols.md +++ b/docs/protocols.md @@ -14,7 +14,7 @@ How to share your magnetic resonance imaging protocols --- - + ## Purpose @@ -32,7 +32,7 @@ Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/p Training guides are available for WIN members and external users. Access the guides below or via the left navigation menu. -[](../protocols/protocols_guide_internal-how-1) [](../protocols/protocols_guide_external) +[]({% link docs/protocols/protocols_guide_internal-how-1.md %}) []({% link docs/protocols/protocols_guide_external.md %}) <!-- ## Citation diff --git a/docs/protocols/protocols_guide_external.md b/docs/protocols/protocols_guide_external.md index 1a3f7d0ef4192b662fcc87ec95a67ce7ae4cfa20..c65aae10af715f20cc28efa7c7276ec2201ed903 100644 --- a/docs/protocols/protocols_guide_external.md +++ b/docs/protocols/protocols_guide_external.md @@ -22,7 +22,7 @@ A guide for external researchers on how to use the Open WIN MR protocols databas ## For external researchers External researchers are able to search the database for MR protocols which research teams have chosen to make openly available. These may be deposited to support publications as supplementary methods material, or they may form the main body of research in sequence development. - + ### 1. Access the MR Protocols database Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/protocols/) diff --git a/docs/protocols/protocols_guide_internal-how-1.md b/docs/protocols/protocols_guide_internal-how-1.md index 2e1ebee2fe259f1d388bd26a3b060b895f27f419..ebc699afe6d20a21ce21ab05f8ee4329d086576f 100644 --- a/docs/protocols/protocols_guide_internal-how-1.md +++ b/docs/protocols/protocols_guide_internal-how-1.md @@ -13,7 +13,7 @@ nav_order: 2 --- -<!--  --> +<!--  --> ## Contents @@ -50,7 +50,7 @@ You might want to add a statement such as "available for re-use, but I'm unable Only WIN members (as determined by SSO authentication) are able to deposit protocols in the database. - + To log in: 1. Go to [https://open.win.ox.ac.uk/protocols/](https://open.win.ox.ac.uk/protocols/) @@ -63,7 +63,7 @@ To log in: Protocols are saved to individual user profiles. - + 1. Once you are logged in, you will see the `Add Protocol` icon. 2. Click on `Add Protocol`, and you will be taken to the `Add new protocol` page. @@ -81,7 +81,7 @@ You can enter details about your protocol which are relevant to the study as a w NOTE: If you are publishing customised pulse sequences, please be sure to indicate your willingness and requirements for sharing them (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences) below). - + ### 3.1 Project, hardware and species Some fields of this section are autmatically retrieved from your pdf and other ones have to be added by selecting the appropriate items from the dropdown menus like: @@ -141,7 +141,7 @@ You can add details specific to individual sequences. These details may make the Each of the sections below should be completed for each sequence. - + ### 5.1 Sequence name This is identified from the pdf. You can update it or add any additional context where necessary. @@ -181,4 +181,4 @@ Add any references which are relevant to this protocol for example the accompany We recommend that you consider using the [CRediT](https://casrai.org/credit/) system for identifying individual author contributions. You may wish to order authors alphabetically. - + diff --git a/docs/protocols/protocols_guide_internal-how-2.md b/docs/protocols/protocols_guide_internal-how-2.md index 7ec823d6234e0ece6212fc86c50195365af1e0a8..6c93f2e9c24dad754bbd053a9e9eb6b8624afa79 100644 --- a/docs/protocols/protocols_guide_internal-how-2.md +++ b/docs/protocols/protocols_guide_internal-how-2.md @@ -13,7 +13,7 @@ nav_order: 3 --- -<!--  --> + <!-- --> We suggest using the free tool Zenodo for creating a Digital Object Identifier (DOI) for your protocol. This will allow others to cite your protocol independently from other work in the study and add contributors who may not be named elsewhere. diff --git a/docs/protocols/protocols_guide_internal-how-3.md b/docs/protocols/protocols_guide_internal-how-3.md index edc0f37c06cedfe03acc775bd502d5385b797710..f4f8d6096ba0f437ed4bc2052123e47d8670dfcf 100644 --- a/docs/protocols/protocols_guide_internal-how-3.md +++ b/docs/protocols/protocols_guide_internal-how-3.md @@ -13,12 +13,12 @@ nav_order: 4 --- -<!--  --> +<!----> If you are using the protocols database to track changes made to your protocol while piloting, you can amend the entry and create a new version that can be reviewed at any point. - + 1. Go to `my protocols` and find the entry you would like to update. 2. Select if you are adding a new protocol pdf file (`Update with new protocol file`) or making changes to other parts of the entry (`Update keeping existing protocol file`) diff --git a/docs/protocols/protocols_guide_internal-how-4.md b/docs/protocols/protocols_guide_internal-how-4.md index 3cb704accda80d7a939fe602b160618554bb2e01..79ca39ff7931a89de7927832c2a094d1af461b12 100644 --- a/docs/protocols/protocols_guide_internal-how-4.md +++ b/docs/protocols/protocols_guide_internal-how-4.md @@ -13,7 +13,7 @@ nav_order: 5 --- -<!--  --> +<!----> You can track how many times your protocol has been viewed and downloaded from the `Engagement Statistics` panel. Views and downloads are separated into internal to Oxford (users have logged in with an SSO) or external. When reporting on the impact of your entry, remember to also include the Zenodo views and downloads statistics, if you have used Zenodo to create a DOI. diff --git a/docs/protocols/protocols_guide_internal-why-use.md b/docs/protocols/protocols_guide_internal-why-use.md index 0ac6ef920edb83984bdfcb6e039d124aee0d842d..4b7708dc82101405ad5cad50a85b796b69b0cb7b 100644 --- a/docs/protocols/protocols_guide_internal-why-use.md +++ b/docs/protocols/protocols_guide_internal-why-use.md @@ -15,20 +15,20 @@ Why you should consider using the WIN MR protocols database to record and share --- -<!--  --> + <!-- --> *The MR protocol database has been developed to share MR protocols internally across WIN as well as externally. The database provides access to standard protocols and to the latest experimental protocols uploaded by WIN members. The database facilitates sharing your MR sequence within and between research groups and helps you to keep track of updates using version control. Each deposited protocol contains all information necessary to reproduce that sequence on an appropriately licensed scanner, allowing yourself and others to have a permanent and full record of your data acquisition methodology.* ## Benefits -### Version control  -The MR Protocols database is version controlled, so WIN members are invited to upload their protocols during piloting to keep track of optimisation and final versions. Comments and notes can be added to each entry so you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data](../../data) server +### Version control  +The MR Protocols database is version controlled, so WIN members are invited to upload their protocols during piloting to keep track of optimisation and final versions. Comments and notes can be added to each entry so you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data]({% link docs/data.md %}) server. -### Citable research output  +### Citable research output  Versions (with minor and major edits) can be assigned a digital object identifier (DOI) using the [Oxford Research Archive (ORA) Data repository](https://deposit.ora.ox.ac.uk) using the stable link provided by the MR Protocols database. Once a DOI has been created, your MR protocol becomes a citable object which you can add to your list of research outputs. -### Reproducible methods detail  +### Reproducible methods detail  Depositing your MR protocol in the database is as simple as uploading the sequence pdf available from the scanner console, or alternatively you can upload the .exar file used by our [Siemens scanners](https://www.win.ox.ac.uk/about/facilities). Sequences' details are captured from either document and parsed into a unified machine readable and searchable format. You can upload a single sequence or all sequences used in a single imaging session (a protocol) together. diff --git a/docs/protocols/protocols_guide_internal.md b/docs/protocols/protocols_guide_internal.md index e8ca57cc913d81dc71f77e65a638c059a04de205..ac79f8a20cf3d508d4ce051d82e497d16f061fe3 100644 --- a/docs/protocols/protocols_guide_internal.md +++ b/docs/protocols/protocols_guide_internal.md @@ -14,4 +14,4 @@ nav_exclude: true --- - +