TeSS is ELIXIR's Training e-Support System, developed by ELIXIR-UK, for disseminating, discovering and packaging training resources, primarily by aggregating information from ELIXIR nodes, but also from various 3rd-party content providers.
New technologies are generating huge amounts of life-science data, which scientists need to transform into new discoveries. However, few researchers have all the right skills to take advantage of this sudden data bonanza.
ELIXIR-UK is responding to this challenge by coordinating European initiatives to training research scientists in computing, statistics and bioinformatics. By plugging the skills gap, ELIXIR-UK aims to strengthen life sciences across Europe and set the agenda for future training needs.
- Niall Beard (TeSS manager, University of Manchester)
- Milo Thurston (TeSS developer, Oxford e-Research Centre)
- Finn Bacall (TeSS developer, University of Manchester)
- Terri Atwood (TeSS co-investigator, University of Manchester)
- Carole Goble (TeSS co-investigator, University of Manchester)
- Susanna-Assunta Sansone (TeSS co-investigator, University of Oxford)
- Aleksandra Nenadic (former TeSS manager, University of Manchester)
How to add your resources
TeSS sources the majority of its training materials and events through aggregation. We do this by creating scripts that extract the metadata about resources from websites. These are ran each night to keep the resource information up to date.
If you have a website with more than 3 training materials or events and wish to add them to TeSS, we can create a script to aggregate from your site. There are several techniques we utilize depending on your websites features.
Please contact our help desk and tell us which format your data is in. If your site does not conform to one of the below formats, please see the schema.org item.
API - An API is a programmatic interface. If you have an API for your website we will write a client to interface with it. This is our preferred method, though we ask you to keep us informed if there are any API changes
Schema.org - schema.org produce schemas to structure data online for search engines to read. schema.org is becoming more prevalent and we recommend this option if you do not have an API or any other option readily available for us.
RSS Feed - An RSS feed is a type of news format. Many sites have RSS feeds which list the recent posts on a site in a standard format. We can write a script to parse this.
ICS (Events only) - An ICS is a calendar feed. If you use Google calendars or a calendar widget on your website you likely have an ICS file which contains the events metadata for the calendar to render. We can write a script to parse this.
Git Repository - A git repository is a directory containing files that can be collaboratively edited. If you are using GitHub (or similar) to develop your training resources and/or use GitHub.io (or similar) to render them, we can write a script that clones the repository and extracts resource information. We may ask you to create a metadata file in YAML format to help us extract the metadata.
SOLR server (or similar) - A solr server is a search engine that many sites use for their internal search functionality. If you have a SOLR server that is publicly accessible, we can write a script to interface with it.
Other - If you have training metadata in another structured format such as an XML or JSON dump, a CSV file, a YAML file, or any other format, we would be happy to write a script to parse it.
TeSS has a read API. Information about request parameters and return objects can be found in our Swagger Hub Documentation. We're still in the process of documenting our full API so bear with us.
As a rule of thumb - You can add .json to the end of most pages to retrieve the data in a common exchange format. e.g.
No - TeSS is a repository of metadata for training materials and events (i.e. a registry of training materials and events). TeSS is an aggregator of metadata of ELIXIR-relevant training information and resources, harvested from individual ELIXIR nodes and from 3rd-party content providers. It does not store original training resources, just the metadata and links to them.
TeSS does not store original training resources itself; rather, it stores metadata of and links to original training resources, and also enables users to create their own packages and workflows of (linked) materials to suit their needs.
TeSS harvests and aggregates training metadata from ELIXIR nodes and from 3rd-party content providers, and filters and displays that information according to different ‘views’ (e.g., ELIXIR overview versus node-specific versus general, etc.) - it does not store the training resources themselves (i.e. it is not a repository - it is a registry).
The GOBLET Training Portal acts a repository of materials and courses, and provides a catalogue of trainers and course organisers. The primary focus of TeSS is on ELIXIR resources and nodes; the principal focus of GOBLET is on the training resources and events of its worldwide members.
Registered users can add a content providers from the content providers page page, by clicking the 'Add content provider' button. In the form provided, write a short description, upload the provider's logo, and provide a link to their website. Typically, this task will be performed by an admin rather than a regular user.
You cannot upload training materials and events directly to TeSS (to do this, we encourage you to use 3rd-party repositories, such as GOBLET).
Registered users of TeSS can, however, add links to training materials manually from the training materials page, by clicking the 'Add training material' button. In the form provided, simply complete the various fields, add a link to the relevant resources and, where appropriate, attribute the content to a particular provider. By doing this, you effectively create what is termed a ‘training material’ in TeSS; this does not contain the actual material, but links to it on the content provider’s website or portal.
Alternatively, as mentioned above, training material and related information and metadata can be ingested automatically using a content provider's API (if such exists), or by contacting the TeSS development team to develop a suitable website scraper.
We disallow manual addition of events to TeSS - you should either register your event with the iAnn event dissemination system or contact the TeSS team to arrange inclusion of your training events automatically via your API or a website scraper.
Training packages in TeSS are bespoke collections of ‘training materials’. For example, you can create a course by making a package of all training materials you plan to use in that course.
This is a two-step process. First, you need to create a package from the packages page. Next, you need to create a link from the relevant training material to that package (note: training materials can belong to several training packages or workflows). To do this, navigate to that particular training resource, select the 'Packages' tab, and select the appropriate package from the drop-down list. This effectively adds the ‘training material’ to the selected package.
In TeSS, training workflows are essentially navigational tools that guide users, step-by-step, through specific types of data analysis (e.g., protein sequence analysis, protein structure analysis, homology modelling, MS-based metabolomic analysis …), highlighting relevant tutorials, lessons, software tools, databases, and so on, relevant to each step of the analysis pipeline. From the available resources, users may select those of particular interest and assemble them into their own customised training packages.
Users may navigate workflows in whatever way they wish, whether step-by-step according to the predefined workflow, or skipping to steps that are more relevant to their training needs.
Funders, groups and people
TeSS is funded by:
- ELIXIR (ELIXIR-EXCELERATE grant by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559)
- BBSRC UK (Delivering ELIXIR-UK grant, grant agreement number BB/L005050/1)
The TeSS team would like to acknowledge the help of a number of groups and individuals and thank them for useful discussions, feedback and help while developing TeSS - to name but a few:
- ELIXIR technical staff and coordinators from the Hub, in particular Rafael Jimenez, Martin Cook and Premysl Velek
- Training coordinators from ELIXIR-NL (Celia van Gelder) and ELIXIR-CH (Patricia Pelagi)
- Structural bioinformatics group (lead by Chistine Orengo and Cath Brooksbank)
- Exome Sequencing workflow, by Sarah Kusala [licenced under Creative Commons Attribution 3.0 Unported (CC BY 3.0)]
- Books HD, by Abhi Sharma [licenced under Creative Commons Attribution 2.0 Generic (CC BY 2.0)]
- Packaging Hager, by Hager Group [licenced under Wikipedia Commons:Licensing]
- University of Manchester - Old and New, by Giuseppe Moscato [licenced under Creative Commons Attribution-NonCommercial-ShareAlike 2.0 Generic (CC BY-NC-SA 2.0)]
TeSS is populated either automatically, by scraping training information from content providers using special scraper scripts which add links to training resources to TeSS, or by adding links to training resources manually by users.
Hence, TeSS consists of the portal software, implemented using the Ruby on Rails framework, and the scraping/aggregation scripts written in Ruby. Both the TeSS portal source code and the scraping/aggregation scripts are open source, licensed under the BSD 3-clause license, and can be found at GitHub.