Squid Repository


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 - Jan 2018

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 Squid3, the help menu provides a link that initializes a new GitHub issue for you - please use freely.

Request The current version is only tested on a few 9-, 10-, and 11-species Prawn xml files. We would like to have more examples of Prawn files and Squid2.5 tasks in Excel for testing.

The current versions - Squid3-0.2.n.jar - prototype the development of the workflow support including project, task, and expression management features of Squid. Squid provides for creating and saving Squid Project files that have an extension of “.squid” and are intended to save the current state 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 currently allows for naming the project, naming the analyst, and reviewing statistics about the Prawn XML file. We encourage you to use it to experiment with managing your Prawn XML files by merging, splitting, and editing them.

The PrawnFile menu provides 1) Audit Session, 2) Audit Masses, and 3) Edit Spots. These give a summary and in-depth look at spots, duplicate names for spots, species statistics, and scans statistics. Edit Spots supports editing spot names, filtering spots by name, and setting both the project’s reference material spots and concentration 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 within the project file but without changing the source XML file.

The Task management functionality provides for customization, parameter-setting, isotope-labeling, ratio-choosing, and expression management. Squid supports importing tasks from Squid2.5 task files - this is a work-in-progress that requires editing of expressions. One key concept to remember is that Squid2.5 conflated “equations” with report columns. Squid 3 separates “expressions” from report columns and thus simplifies expressions and reduces the population of them.

Thank you in advance for any suggestions you contribute. We are available for walk-throughs, etc. if needed to help convince you to participate and contribute.

Additional features will appear over time and may not be documented here concurrently. Please be patient and contribute your ideas via the issues tracker.

Updated 2 Jan 2018