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MetaLIMS, A Simple Open-Source Laboratory Information Management System for Small Metagenomic Labs

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# Notice
MetaLIMS is no longer being actively maintained. Current applications mentioned may be out of date. While users are encouraged to use the most recent versions (Ubuntu, MySQL, PHP, Apache) possible for all deployments, MetaLIMS has not been updated for changes in recent updates. Usage remains at the user's own discretion.

# MetaLIMS, A Simple Open-Source Laboratory Information Management System for Small Metagenomic Labs

## MetaLIMS v2 Installation and Usage
### Home
*    [About](https://github.com/cheinle/MetaLIMS/wiki/)

### Installation
*    [Installation Decision Tree](https://github.com/cheinle/MetaLIMS/wiki/installation-decision-tree)
*    [MetaLIMS v2.0 Hosted Installation (via AWS Lightsail)](https://github.com/cheinle/MetaLIMS/wiki/MetaLIMS--v2.0-Hosted-Installation-(via-AWS-Lightsail))
*    [MetaLIMS v2.0 Full Manual Installation](https://github.com/cheinle/MetaLIMS/wiki/MetaLIMS--v2.0-Full-Manual-Installation)

### Manual
*    [MetaLIMS v2.0 Manual For Admin](https://github.com/cheinle/MetaLIMS/wiki/MetaLIMS-v2.0-Manual-For-Admin)
*    [MetaLIMS v2.0 Manual For Basic Usage](https://github.com/cheinle/MetaLIMS/wiki/MetaLIMS-v2.0-Manual-For-Basic-Usage)
*    [MetaLIMS v2.0 Manual For Developers](https://github.com/cheinle/MetaLIMS/wiki/MetaLIMS-v2.0-Manual-For-Developers)

### Misc  
*    [lamp.sh](https://github.com/cheinle/MetaLIMS/wiki/lamp.sh)
*    [apache_ssl_16.sh](https://github.com/cheinle/MetaLIMS/wiki/apache_ss_16.sh)
*    [metalims.sh](https://github.com/cheinle/MetaLIMS/wiki/metalims.sh)

##Synopsis

Laboratory Information Management Systems (LIMS) have grown and changed over the years from simple reporting tools to more elaborate packages including instrument integration, analysis, and complex workflows. At its most basic, LIMS allows users to easily record and access various sample metadata. As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects, and must take on the complexity of data storage for high volumes of samples. This has created a need for low cost LIMS that contain flexible input fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated IT position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. 
 
MetaLIMS is a free and open source web-based application that is available for deployment and customization via GitHub at no cost. MetaLIMS focus is to store sample collection and processing metadata prior to sequencing and analysis pipelines. MetaLIMS was built with the intended use by environmental metagenomics labs and in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the users lab. MetaLIMS can produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web-deployment, MetaLIMS suggests use of commercial web-hosting combined with easy to use MetaLIMS bash scripts for ease of set-up. MetaLIMS documentation gives examples using one product, Amazon Web Services Lightsail.
 
MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open source tool that also has the flexibility to meet individual lab needs by allowing custom recording fields. MetaLIMS manages simple installation through use of easy to run bash scripts combined with suggested web-hosting for simple deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.

##Authors/Contact Info

Cassie Heinle

cheinle@ntu.edu.sg

Singapore Center For Environmental Life Sciences and Engineering

Nanyang Technological University

www.scelse.sg

Email bugs and feature requests to: cheinle@ntu.edu.sg

##License
[Read LICENSE] (https://github.com/cheinle/MetaLIMS/blob/master/license.md)

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