Dedicated to the sharing of scientific data
Scientists in the neuroscience community connected to the Barres Lab at Stanford University needed a new website dedicated to sharing scientific data. Renound neuroscientist Ben Barres was of the belief that datasets generated in his lab should be shared with the broader neuroscience community. After unsuccessfully trying a few different developers and software teams, Emory University in the US contacted the team at Arttia Creative to assist with bringing there vision to life. We were more than happy to help.
PROJECT BRIEF
BrainRNAseq is a site dedicated to sharing scientific data. From its inception, the client's goal was to create a database that was simple to use, access, and interpret.
To that end, the client curated datasets that were amenable to quick and easy interpretation. Because of the rebuilt website's simplicity, visitors are encouraged to supplement the information with the numerous other databases that exist in the field of brain transcriptomics/proteomics.
Arttia Creative also created a tool to enable other researchers to create similar websites to share their own data, thus making data accessibility easy and standardised for all skill levels. This needed to be a low or no-cost way for researchers to create their own website interface using their own data.
Expertise delivered
- Website consultancy
- Website wire-frames
- Website code and development
- Data mapping consultancy
- Website interface layout and design
- Custom WordPress plugin development
- Database manipulation and management
- Complex data search functions
- Search with any gene symbol
- Automatically populate and display Homologs for any additional species
- Logo design for Webseq information website
Delivering a website project that no-one else could!
The client had approached more than 10 providers who were unable to provide a solution for their project. Passing the challenge to the team at Arttia Creative who imagined and delivered an opensource, effective and enabling solution.
Making data accessibility an easy and standardised process for all skill levels
Arttia Creative was tasked with recreating the old and out-of-date Python website that showcased various datasets collected in the Ben Barres lab. The old website never quite had the functionality needed to build the data sets in the most useful way.
This substantial website development project required database expertise and user interface design knowledge. We created a unique website that displays the datasets as graphs, with the option to download the source data and display the relevant citations.
By adding a reference database, we fine-tuned the search function and enabled search with any gene symbol to visualise its expression across both mouse and human CNS cell types.
We also added the ability to automatically populate and display Homologs for any additional species, which wasn't included in the old version. This is a great addition for users and visitors.
Unique datasets manager plugin
Arttia Creative then used the website as a model to create a tool for anyone to create a similar website to share their data as per Ben Barres's vision.
Arttia Creative developed a unique custom-coded WordPress plugin to handle the datasets and display them as graphs on a WordPress webpage by simply adding a shortcode to the page. A ‘search’ box and ‘search terms’ box can also be added through a shortcode.
Shortcodes are also available to add a search box and a search terms box, making the page setup easily customisable by anyone on their own WordPress website.
To create the datasets, the plugin allows you to specify the required headers for the dataset by adding the Species and Groups. It then creates a custom CSV with that information to download and populate with your own data.
To complete the process, you upload this CSV and generate the shortcode to display the dataset on a website page. The dataset's display can be customized by specifying labels and various other settings, like font size and margins.
We also built in the ability to upload a reference database so that the datasets could be searched using a gene symbol to visualise its expression across human and mouse CNS cell types. Again, this is something that wasn't available in the old setup.
The plugin can easily handle large data files and includes a default reference CSV for the search functions. This was very complex to achieve, and we congratulate our WordPress development team on their achievement!
Your international life sciences brand and website design consultancy
Datasets in action
Neuroscience Data Set Technology Stack
We used a specific set of technologies to develop the Datasets Manager WordPress plugin. Here's a detailed breakdown:
- Backend: PHP WordPress
- Database: MySQL
- Web Server: Nginx
- Frontend: HTML, CSS, JS
- Quality Assurance (QA): Manual testing using real devices
- Project Management: Jira, BitBucket
Challenges and Requirements
Previously, Brain RNA Seq performed all calculations and reporting off-site using Microsoft Excel. This method was inefficient and prevented real-time data access.
The challenge was creating a system that automated these processes, directly allowing real-time data manipulation and visualization on their website.
Solution Implementation
We designed the Datasets Manager plugin to address the client's needs effectively. The plugin now allows users to:
- Automated Calculations: The plugin performs all necessary calculations automatically upon data input.
- Standard Deviation
- Standard Deviation Mean
- Mean of all values of a specific dataset
- Density of a certain dataset
- Grading of all values for graph representation
- CSV Data Import: Users can now import data via CSV files, eliminating the need for manual data entry.
- Graphical Data Representation: The plugin generated visual graphs, providing clear and immediate insights into the datasets.
Development Process
We followed a structured development process using the Scrum methodology to ensure efficiency and adaptability:
- Planning: We gathered detailed requirements and created a project roadmap.
- Development: Our team developed the backend using PHP WordPress and the frontend using HTML, CSS, and JS.
- Testing: We conducted manual testing on real devices to ensure the plugin's functionality and reliability.
- Deployment: The plugin was deployed on an Nginx server, with ongoing project management and version control through Jira and BitBucket.
Development Outcome
The development of the Datasets Manager plugin significantly improved Brain RNA Seq's workflow. Key benefits included:
- Time Efficiency: The plugin reduced the time needed for complex calculations and report generation, previously done manually with Excel.
- Multiple Dataset Management: Users can upload and process multiple datasets simultaneously, increasing efficiency and productivity.
- Comprehensive Statistical Analysis: The plugin displays various statistical measures, such as mean, median, and standard deviation, offering comprehensive data insights.
- Customization Options: Users can customize display options and color schemes, allowing for tailored data visualization.
- Easy Integration: Shortcode support enables easy integration of datasets into WordPress posts and pages, which enhances usability.