Bika LIMS in the 2015 Google Summer of Code

This year, the Bika Open Source LIMS Collective is 1 of 137 organisations mentoring in the Google Summer of Code initiative, GSoC 2015


Other accepted organisations include the A to Z of FOSS big names, Apache, Debian, Django, Drupal, FreeBSD, Git, ..., Postgres, Python, R, Ruby, Samba, Wikimedia, X. Thank you Google! Mentors. The Best Jordi Puiggené, backed by Campbell McKellar Basset, are putting Bika LIMS out on their limbs in the upcoming Google Summer of code 2015, mentoring students May 25 - August 24. Applications Applications are open from 16 to 27 March, Google Summer of Code 2015. More information on Bika's opportunities at the wiki, GSoC 2015 and Instructions for Students. Please propose 3 month coding projects around the Bika Ideas list approved for the program. Skills required Medium to high Python, Plone, ZODB, Zope Page Templates, jQuery, D3.js for graphing, CSS. Familiarity with Bika LIMS is a plus. Stipends Successful applicants earn a stipend of $5500! at successful completion of their project. They stand to learn a lot, regardless, under the stringent review and delivery regime applied... The Bika mentors get $500;-) each, and the project a whole lot of quality code. We are looking forward to work with you. And thanks Jordi, Campbell!	Bika GSoC 2015 Ideas list Froid. Free Open Instrument Middleware The Open Instrument Middleware will be a free-standing instrument server to easily interface any laboratory instrument to any laboratory software. Though the current Bika LIMS interface module was designed with this in mind and can be used as a basis, see Creating an Instrument Import Interface, Froid will be vendor neutral to attract as many interfaces possible, all open sourced on the AGPL for protection. One of its main functions will be to resolve serial RS232 communications with laboratory instruments. See the initial top level design at Froid. Free Open Instrument Middleware. Fluffy and dated Functional Specification. Android Samp. Free and Open Sampling App Bika LIMS has some lab forms running on Android for labs without enough desk space for bigger hardware. There's demand for a standalone app to use in remote sampling locations, e.g. health care, biobanking and geological exploration, which can then be synced with online servers when the app gets in range. It should capture sampling point / patient details, take photos and GPS coordinates, record field analyses. Android Samp. Free and Open sampling App discussion document. Inventory and Supply Chain Management While Bika LIMS already has the basics for Product and QC Reference Standard management, as well as some simple Supply Orders functionality, this module has been neglected for too long. Inventory and Supply Management top level design discussion document. Productivity, Management and Tracking Reports Bika LIMS already covers most of the functions required in a laboratory workflow, but lacks a dashboard, and the generation of reports matching the system's database evolution, daily-usage reporting and tracking charts among others. Bika Health FDA 21 CFR Part 11 customisations Bika Health LIS is a Plone extension that adds health care functionality to Bika's industry standard Micro-Biology and Chemistry. Patients, Doctors, Referring Institutes, Clinical Cases, medical history, interfaces with clinical instruments and EMR or hospital systems. It forms the basis of Bika for bioinformatics and is also used in veterinary settings with animal subjects and veterinarians in as patients and doctors. Through customisations done for the ISO 17025 and CLIA standards earlier, Bika Health fulfills 70% of the FDA's 21 CFR Part 11 requirements. See gap analysis, 21 CFR Part 11 LIMS Requirements - Electronic signatures and records. The 'idea' is to close that down. SQL back-end Bika LIMS uses Plone's native and powerful object-oriented database ZODB as default Database Management System and provides a JSON-API to integrate the system with others, mainly ERPs. Some peers use relational databases such as PostgreSQL and labs would find Bika LIMS easier to integrate if it supported SQL databases. Lab managers also prefer data in tabular format they can access with their SQL query tools of choice. EduLIMS add-on for Bika LIMS A Bika add-on specifically for educational centers, private or public, such as high schools, colleges, universities and technology centers. EduLIMS focuses on activity tracking and evaluation of trainees, in the use LIMS itself and at the same time, learn the basics of a lab workflow, including procedures, QA/QC, instrument management, etc.

Other accepted organisations include the A to Z of FOSS big names, Apache, Debian, Django, Drupal, FreeBSD, Git, ..., Postgres, Python, R, Ruby, Samba, Wikimedia, X.

Thank you Google!

Mentors. The Best

Jordi Puiggené, backed by Campbell McKellar Basset, are putting Bika LIMS out on their limbs in the upcoming Google Summer of code 2015, mentoring students May 25 - August 24.

Applications

Applications are open from 16 to 27 March, Google Summer of Code 2015. More information on Bika's opportunities at the wiki, GSoC 2015 and Instructions for Students. Please propose 3 month coding projects around the Bika Ideas list approved for the program.

Skills required

Medium to high Python, Plone, ZODB, Zope Page Templates, jQuery, D3.js for graphing, CSS. Familiarity with Bika LIMS is a plus.

Stipends

Successful applicants earn a stipend of $5500! at successful completion of their project. They stand to learn a lot, regardless, under the stringent review and delivery regime applied... The Bika mentors get $500;-) each, and the project a whole lot of quality code.

We are looking forward to work with you. And thanks Jordi, Campbell!

Bika GSoC 2015 Ideas list

Froid. Free Open Instrument Middleware

The Open Instrument Middleware will be a free-standing instrument server to easily interface any laboratory instrument to any laboratory software.

Though the current Bika LIMS interface module was designed with this in mind and can be used as a basis, see Creating an Instrument Import Interface, Froid will be vendor neutral to attract as many interfaces possible, all open sourced on the AGPL for protection.

One of its main functions will be to resolve serial RS232 communications with laboratory instruments. See the initial top level design at Froid. Free Open Instrument Middleware. Fluffy and dated Functional Specification.

Android Samp. Free and Open Sampling App

Bika LIMS has some lab forms running on Android for labs without enough desk space for bigger hardware.

There's demand for a standalone app to use in remote sampling locations, e.g. health care, biobanking and geological exploration, which can then be synced with online servers when the app gets in range.

It should capture sampling point / patient details, take photos and GPS coordinates, record field analyses.

Android Samp. Free and Open sampling App discussion document.

Inventory and Supply Chain Management

While Bika LIMS already has the basics for Product and QC Reference Standard management, as well as some simple Supply Orders functionality, this module has been neglected for too long.

Inventory and Supply Management top level design discussion document.

Productivity, Management and Tracking Reports

Bika LIMS already covers most of the functions required in a laboratory workflow, but lacks a dashboard, and the generation of reports matching the system's database evolution, daily-usage reporting and tracking charts among others.

Bika Health FDA 21 CFR Part 11 customisations

Bika Health LIS is a Plone extension that adds health care functionality to Bika's industry standard Micro-Biology and Chemistry. Patients, Doctors, Referring Institutes, Clinical Cases, medical history, interfaces with clinical instruments and EMR or hospital systems.

It forms the basis of Bika for bioinformatics and is also used in veterinary settings with animal subjects and veterinarians in as patients and doctors.

Through customisations done for the ISO 17025 and CLIA standards earlier, Bika Health fulfills 70% of the FDA's 21 CFR Part 11 requirements. See gap analysis, 21 CFR Part 11 LIMS Requirements - Electronic signatures and records. The 'idea' is to close that down.

SQL back-end

Bika LIMS uses Plone's native and powerful object-oriented database ZODB as default Database Management System and provides a JSON-API to integrate the system with others, mainly ERPs.

Some peers use relational databases such as PostgreSQL and labs would find Bika LIMS easier to integrate if it supported SQL databases. Lab managers also prefer data in tabular format they can access with their SQL query tools of choice.

EduLIMS add-on for Bika LIMS

A Bika add-on specifically for educational centers, private or public, such as high schools, colleges, universities and technology centers.

EduLIMS focuses on activity tracking and evaluation of trainees, in the use LIMS itself and at the same time, learn the basics of a lab workflow, including procedures, QA/QC, instrument management, etc.