This is the first major release of Apache Taverna since joining the
Apache Software Foundation incubator.

Suitable for people in research, industry, for students, DIYbio and more. Relevant for people at any stage in their career looking to expand their knowledge and skills in synthetic biology and genome engineering.

Course runs from Sunday 3rd July – Saturday 9th July 2016.

Learn about synthetic pathway and genome optimisation and design from international experts, by participating in an innovative lab course covering recent breakthroughs in synthetic biology and synthetic genomes including: Synthetic chromosome design and assembly CRISPR-mediated genome engineering Synthetic pathway design and assembly SCRaMbLE-mediated synthetic genome rearrangement State-of-the-art lab automation and design software.

Accommodation included from Sunday 3rd July to Saturday 9th July (Check out on the 10th).

Package includes the 5th annual Sc2.0 and Synthetic Genomes conference with major synthetic biology and yeast research speakers including:

·         Jef Boeke – New York University

·         Jim Collins – MIT and the Harvard Medical School

·         Pam Silver – Harvard Medical School

·         Jasper Rine – UC Berkeley Maitreya Dunham – University of Washington

·         Romain Koszul – Institut Pasteur Matthew Wook Chang – National University of Singapore

·         Tom Ellis – Imperial College London

·         Patrick Cai – University of Edinburgh

·         Additional speakers TBC.

Price Per Person: £420. This includes all accommodation, meals and conference attendance. A limited number of travel awards and bursaries will be available. 

For more information the summer course website: https://syntheticgenomes.wordpress.com

Join our new webinar series launching Mon 25th Jan 2pm-2.45pm GMT. Our guest speaker for the first session will be Steven Wiley.

To find our more about the webinar visit our webinar page.

This version of SEEK forms the base version for our new FAIRDOMHUB service, about which we will be releasing more details in the new year.

Included in this version are some key new features:

* Support for the self creation and administration of Programmes, and Projects within them. If this feature is enabled, users will be able to setup their own Programmes and support them without the need of a full SEEK administrator other than the initial activation.
* A refinement of the administrative roles.
* Publishing of entire Investigations as Snapshots – frozen in time as Research Objects, along with a DOI. In the future we will be extending this to also support more fine-grained Studies and Assays.
* For more details about this release please visit http://fair-dom.org/news-seek-1.0

http://biosb.nl/education/course-portfolio/course-managing-and-integrating-information-in-the-life-sciences/

The showcase is called "Predictive modelling of mosquito-borne diseases in Sweden" and demonstrates how predictions of climate change can be used, together with species distribution information, to predict potential future disease areas. 

http://tinyurl.com/najdjrq

A production-suitable command line tool [4]
=======================================

This proposed GSOC project is to formalize the command line interface for Taverna Language so that it can achieve some of the below:

a) In collaboration with dev@taverna and the mentor, define command line options for workflow conversions and inspection
b) Find and use an appropriate command line parser library
c) –help
d) Basic error handling (e.g. file not found)
e) Batch processing – e.g. recursive conversions
f) Arguments for choosing input and output formats
g) Unit and Integration Tests for the above (ideally through Maven)
The project can be extended by exposing other parts of the API that don't currently have a command line equivalent, e.g.
h) Workflow validation
i) Workflow statistics (number of processors, links, etc)

A databundle viewer [5]
===================

This GSOC project proposes to create a web-based presentation (but not edit) of a workflow run, e.g. the following user story:

1) User uploads the databundle file for a workflow run (or provides the URI to one existing elsewhere) into the presentation system
2) The presentation system shows basic information about the workflow run
3) User navigates to inputs/outputs
4) The presentation system presents a list of inputs or outputs – embedding images etc. where possible, download links for large files, inline for small text, etc
5) User downloads a selected data file

Metadata provided can be presented in many different ways, for instance:

a) Which workflow was executed?
b) Which steps were executed?
c) What step produced this value?
d) What values were produced by this step?
e) What steps used this value?

OGC WPS support [6]
===============

This proposed GSOC project is to, in collaboration with dev@taverna and the mentor

(a) Improve/complete the existing Taverna 2.5 WPS prototype support
Discovery of WPS services from a user-specified WPS server
Configuration of WPS services
Execution of WPS services
(b) Test WPS support using pre-selected WPS servers and services
(c) Migrate the WPS support to the Taverna 3 codebase
(c) Document the Taverna 3 WPS service support

An Android App for Taverna [7]
==========================

The project would be to:

Extend and complete Taverna Mobile: an Android app to run Taverna
workflows available on myExperiment (http://www.myexperiment.org)
using Taverna Server.

1) fix the ssl/https parts and use the latest version of taverna server
2) update the code to remove some legacy dependencies and use the
latest APIs
3) improve the UI and responsiveness

============================

If you, or any students you know, are interested in these or any other Taverna projects, then please discuss ideas on the Taverna developers' list dev@taverna.incubator.apache.org and then submit proposals to Google by 27th March. More information is in the GSOC 2015 FAQ [8]

Alan

[1] https://www.google-melange.com/gsoc/homepage/google/gsoc2015
[2] http://bit.ly/1BCUgjU
[3] http://bit.ly/1EebXXp
[4] https://issues.apache.org/jira/browse/COMDEV-120
[5] https://issues.apache.org/jira/browse/COMDEV-121
[6] https://issues.apache.org/jira/browse/COMDEV-122
[7] https://issues.apache.org/jira/browse/COMDEV-123
[8] https://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2015/help_page 

The format is related to that for Research Objects  http://www.researchobject.org/ and there is a conversion tool between them.