SEEK is an open-source, web-based platform and suite of software tools for the management, linking, exploration and exchange of Systems Biology data, models and Standard Operating Procedures (SOPs). SEEK is designed to facilitate data sharing and collaborations between scientists.
If you have been using SEEK in your research then the key paper to cite is:
Wolstencroft K, Owen S, du Preez F, Krebs O, Mueller W, Goble CA, Snoep JL (2011) The SEEK: A Platform for Sharing Data and Models in Systems Biology, Methods in Enzymology, Volume 500: 629-655 PUBMED: 21943917
We welcome many contributions to our SEEK software. It is possible to easily contribute to both the software or the documentation through GitHub.
Details on how to contribute to SEEK can be found at http://docs.seek4science.org/contributing.html
You can also contribute at a higher level to FAIRDOM in general - details of which can be found at http://fair-dom.org/contribute/.
SysMO-DB was the original project that created SEEK. It was designed to support the SysMO Consortium (Systems Biology for Micro-Organisms), but the principles and methods employed are equally applicable to other multi-site Systems Biology projects. For more information please visit http://www.sysmo-db.org/
The term 'data' covers
The JERM is our Just Enough Results Model for describing results and the relationships between them.
You can find out all about the JERM and our templates built around it at Just Enough Results Model.
Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations.
More about ISA here http://isacommons.org/
Yes. Under the “Yellow pages” tab you can access a directory of people, project and institutions. Here you will find information including expertise, affiliations, contact details, and the associated data.
SEEK is a platform that allows data sharing through the full lifecycle of a project, and across projects. It allows you to catalogue your data during the early stages of creation, share with other members of your project when needed, and make public on publication or when suitable. This allows you to catalogue all of your data in one place, and share easily with relevant parties. Moreover, SEEK provides you bundle of tools to analyse the data, simulate the models, view the document directly
Sharing your data allows others to access and use it in ways you may not. This maximises the feasible contributions you and your data can make to the science community.
To add data to your profile click on the “create” button in the top left corner of the screen. From there you can select the type of data you want to upload and then submit it in a suitable format upon request.
Yes, the data uploaded into SEEK are kept in SEEK. Where the data are stored elsewhere (e.g. a publication) a description of the data and a link can be used. In this instance, the actual data are not stored in SEEK.
When you sign up to SEEK, your profile will be associated with relevant projects. All data have to be linked to a person and project, therefore only data relevant to specific projects can be uploaded.
If data changes slightly you can upload a new version of the data to the same entry within SEEK. Visitors to that entry will automatically be presented with the newer version.
If you wish to, and have the correct permissions, you can delete data.If they are associated with other assets or assays, you may first have to remove the associations, otherwise you will be unable to delete it.
No. You will only be able to see data that is shared with you, this includes
Data can be shared such that only information about the data is visible, or so that the data itself can also be downloaded. If you can read information about the data, but not access the data itself, you may contact the data holder directly to request permission using the “request permission” button.
Any data uploaded can be downloaded, provided you have access permission. Where data are linked via a URL, you will have to follow the URL to access the data.
SEEK is built on the secure Ruby on Rails framework, and it is updated regularly and secured through https. We recommend that users use unique passwords.
If you can see and item, but do not have download access, there is a request button, which you can use to submit a request for the data. When doing so, an email will be sent to the owner of the data.
You can of course also contact the author directly, if they have provided contact details in SEEK.
Yes, you can add data as a URL, which is common in the case of publications.
Yes, you can use a RESTful API to access the data within SEEK, and export as XML or RDF. Some data is also exported as Comma Seperated Values (CSV). We will be publishing more on how to access SEEK using APIs in the future.
In the meantime, please contact us on our development mailing list, details of which can be found at http://seek4science.org/contact - doing so means you can give direct input and request changes before the API is finalised and released.
Yes, please visit our Getting SEEK page for information on how to install your own copy of SEEK. You also have the option to download a Virtual Machine image if you wish to try out a SEEK installation quickly.