Welcome to the slivka-bio home server at the University of Dundee

Slivka is a free middleware which provides convenient remote access to computer programs installed on your local computer, a server, or a cluster.

This installation of slivka, maintained by the Barton Group in the Division of Computational Biology, at the School of Life Sciences, University of Dundee, offers web services that wrap a range of bioinformatic programs. These include multiple sequence alignment programs such as Clustal Omega, Clustal W, MAFFT, MUSCLE, T-Coffee, ProbCons and MSAProbs; protein disorder prediction tools: GlobPlot, DisEMBL, IUPred, Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished). It also provides access to secondary structure predictions of proteins via JPred and calculation of amino acid alignment conservation with AACon.

Slivka-bio's web services are designed for easy programmatic access and interoperation. They can be employed with future version 2.12 of the Jalview interactive multiple sequence alignment workbench (via Jalview Desktop or JalviewJS), the Slivka Command Line Client, or directly through the REST API. You can perform computations on your sequences using our publicly available server running at the University of Dundee. Alternatively, you can install Slivka-bio on your local computer, server or cluster to take advantage of your own computing resources.

For Users
If you want to access public or private Slivka services from the command line or programmatically from Python scripts use slivka python client. It also provides tools for interoperability with Jupyter notebook interactive forms located in the nb_utils submodule.
For System Administrators
If you want to host your own bioinformatic services, you should install the slivka-bio package on your machine. If you'd like to create and customise your own services, take a look at slivka's documentation.
For Developers
If you are developing client-side software, it can communicate with Slivka servers directly via the REST API or you can use one of the wrappers for Python and Java.
The slivka project is currently being developed in the Barton Group at the School of Life Sciences, University of Dundee. Development by: Mateusz M. Warowny, James B. Procter and Geoff Barton.
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee
Dow Street
Dundee, DD1 5EH
Scotland, UK
Stuart A. MacGowan, Fábio Madeira, Thiago Britto‐Borges, Mateusz Warowny, Alexey Drozdetskiy, James B. Procter, Geoffrey J. Barton, The Dundee Resource for Sequence Analysis and Structure Prediction, Protein Science, 2019, https://doi.org/10.1002/pro.3783

The current funding for Slivka development is provided by UKRI BBSRC Bioinformatics and Biological Resources Grant: "The Dundee Resource for Sequence Analysis and Structure Prediction" 2018 to 2023 (BB/R014752/1) to Prof. Geoff Barton.