Squid 3.0 was proposed as the project name for replacing Squid 2.50 during the VIII SHRIMP 2016 Workshop in Granada.
Since early 2016, Jim Bowring and Simon Bodorkos produced the open-source program Calamari as a proof-of-concept that we could successfully port the arithmetic of Ken Ludwig’s Squid 2.5 to Java. Simon has documented that effort here.
The details of Simon’s explorations and explanations of Squid 2.5 to date are found here: SHRIMP data processing.
The program Calamari is explained here.
The latest version of Calamari is here.
Development - May 2017
Squid3 development is hosted on GitHub.com and is iterative and community-driven. We encourage you to download and evaluate the latest release, the “.jar” file found here. Squid requires Java 1.8 or later.
To contribute issues and feedback, please join GitHub here. While using Squid, the help menu provides a link that initializes a new GitHub issue for you - please use freely.
The current versions - Squid3-0.0.n.jar - prototype the development of the project-management feature of Squid. Squid provides for creating and saving Squid Project files that have an extension of “.squid” and are intended to save the current sate of work on a project.
The Project menu provides for creating a new project from a single Prawn XML file or by joining together two Prawn XML files. The project manager allows for naming the project, naming the analyst, and reviewing, editing, and splitting the Prawn XML file.
Three tabs show 1) Session Summary, 2) Session Audit, and 3) Manage Spots. The Session tabs provide a summary and in-depth look at spots, duplicate names for spots, species statistics, and scans statistics. The Manage Spots tab supports editing spot names, filtering spots by name, and setting the project’s reference material spots by using the same filtering feature. The context menu on the left-side list is accessed by a right-mouse click and has items for removing a spot and splitting the Prawn file into two files. Any modifications to the Prawn file can be saved to a new Prawn XML file if needed. Note that saving the project preserves the changes to the Prawn XML data.
The Project management functionality is a work-in-progress. We encourage you to use it to experiment with managing your Prawn XML files by merging, splitting, and editing them. Thank you in advance for any suggestions you contribute.