The BTN website (http://www.biotnet.org/
) is a centralized resource for the bioinformatics community to share training materials and techniques, and to disseminate awareness and spark new discussions and initiatives. The global community is welcome to browse the site, and we encourage, in particular, those who are interested or involved in bioinformatics training to join the BTN. All materials in the BTN are made freely available under the Creative Commons Attribution-Share Alike 2.5 License (http://creativecommons.org/licenses/by-sa/2.5/
). The site has been developed by the European Bioinformatics Institute (EMBL-EBI http://www.ebi.ac.uk/
), using the Open Source content management system Drupal (http://drupal.org/
). To facilitate searching, a key feature of the site is the use of tag words. These are currently added as free text when users upload their materials, but ultimately will be compiled into a controlled vocabulary reflecting the most frequently used terminology and using available established ontologies when appropriate. All terms used as tags are searchable, allowing users to sort information at all levels. This facilitates efficient exploration, leading users more rapidly to relevant information (e.g. tag ‘PhD’: by clicking on the term PhD, users obtain details of all trainers registered with the site who provide training for PhD students). The five main areas of the BTN website are described in detail below.
Trainers and organizers
This section lists individuals who have registered to contribute to the site and are involved in bioinformatics training; this includes not only those delivering training sessions directly, but also those involved in the organization and planning of such training. The rationale behind this is 2-fold: first, to build up a community in which trainers can identify each other and share areas of expertise, and in which they can liaise with, and get help from, other trainers; second, to function as a hub for course organizers to identify potential trainers for specific subjects and levels.
This section is the main focus of the BTN site. This section is a direct response to the often-voiced desire to have a common repository of well-documented, open-source training materials. It is specifically intended to help bioinformatics trainers to share, adapt and develop materials, and to make them freely available to the community at large. It is hoped that both having a centralized repository and fostering a culture of sharing will help new ideas and best practices to be readily and rapidly disseminated. To this end, trainers have the opportunity to rank each other's materials, in a similar way to the Amazon ranking system. This includes a comments box to allow trainers to state exactly what was rated and the reason for the given rankings. This functionality aims to stimulate constructive feedback and, consequently, to help improve the quality and timeliness of materials available from the site ().
Figure 1: Screen dump of one of the BTN web pages showing the section about “Training Materials” containing a top level list of topics (categories), a list of the most recently updated materials (on the left) and a list of the most rated materials (more ...)
Training materials are grouped into 10 major categories, according to the types of data handled by different tools and resources: Genes and Genomes; Proteins and Proteomes; RNAs and Transcriptomes; Interactions and Pathways; Small molecules and Metabolomes; Ontologies; Literature and Text mining; Programming and Operating Systems; Biostatistics; and Other. Where appropriate, materials can be tagged to more than one section (e.g. ‘drug discovery’ is relevant to both proteins and small molecules). These categories have been derived from extensive discussions among the contributing authors. However, as the site grows and the community enlarges, the categories will doubtless evolve to reflect wider community needs and interests. Special care will be taken to monitor the content of the ‘Other’ section, to avoid this growing amorphously, and making it more and more difficult to find relevant materials within it.
Anyone can readily access and download materials from the BTN site without a requirement for registration. However, to upload information, registration is necessary. To register, contributors need only provide a brief motivation: this is required in order to ensure that requests are genuine. Apart from a textual description, uploaded materials can include files with any of the following extensions: ppt, pptx, doc, docx, xls, xlsx, pdf, txt. Other formats (e.g. videos) can be incorporated as external hyperlinks. At present, the maximum file size allowed per upload is 64 MB.
While aiming to provide a comprehensive repository of training materials, the BTN nevertheless wishes to avoid redundancy. Therefore, for those who want to share materials but already have a location from which these are available, the BTN site offers the ability simply to add a link to remote material rather than requiring them to be uploaded again. The materials, links and classifications (especially the ‘Other’ section) will be reviewed periodically by appointed BTN members to provide the greatest functionality to the community, while retaining system security and ensuring that the BTN works within system capacities.
Finally, to minimize the risk that the BTN accumulates dysfunctional or outdated materials, automatically generated e-mails will be sent to the submitter 2 years after the submission date asking them to either confirm that their materials are still valid and useful or to agree to the deletion of their materials from the site.
By sharing our own trainer experiences, it emerged how challenging it can be to get a quick overview of available IT-training facilities and appropriate venues (worldwide). This section was created to allow course organizers and providers to list facilities suitable for hosting bioinformatics training events. At the moment, this is a simple list containing the venue name, location, a brief description, and the relevant contact details. In the future, as the community grows, a map view will also be developed to allow rapid identification of suitable venues, together with the contact details of the responsible organization/institute.
Courses and events
Raising awareness of training events is often a significant task for course organizers. Although the primary intention of the BTN site is to address the needs of trainers and course organizers, it emerged from our discussions that being able to identify other courses in the same field would allow potential trainees to locate courses running elsewhere if, for example, a course of interest was fully booked/cancelled, or if his/her expectations were not matched by the learning objectives of the chosen course. This section is not intended to be a holding place for event websites. Instead, it will act as a bill-board for upcoming events, listing a minimal set of information to allow users to decide whether particular events are relevant to them, plus a hyperlink to the actual event website. This could be useful if, for example, during a course, trainers could point to the BTN as the place where trainees could access all the materials, as any uploaded materials could be searched for using the relevant course-name tag. This would have the additional effect of providing indirect access to the course for remote trainers, allowing them to see what type of material is being taught and where. At present, the list of events can be sorted by title, venue or date. Ultimately, the aim is also to integrate this into a calendar view option.
This section lists the URLs of bioinformatics training providers, promotes awareness and allows informal networking and exchange of experiences. It also represents a platform to discuss new ideas and initiate white papers on best practices.