Overview
BioInfoRx offer a variety of cloud-based systems for both academic and industrial scientific research laboratories.
Websites & Intranets
- Research lab websites with matching styles
- Companion websites for scientific publications
- Business websites with integrated e-commerce solutions
Scientific Systems
- Custom item and sample tracking systems for different customers
- Complex lims for biomarker discovery, oligo synthesis
- Project information management with file sharing, messages, tasks
Workflow Automation
- Automation of antibody production process
- Automation of oligo design, synthesis, ordering, and storage
- Automation of transgenic animal production
Big Data Processing
- Complex information Systems for diabetes research laboratories
- Large scale metabolomic and proteomic data analysis
- Analysis and visualization of genomic data, pathways, and enrichment
Websites and Intranets
BioInfoRx offers website development services to academic and industrial customers, including, but not limited to:
- Academic lab websites with compatible styles to department or university websites
- Companion websites for publication purpose, e.g., public databases
- Business websites with integrated e-commerce solutions
- Intranet solutions with web tools for lab information management and process automation
Sample Research Lab Websites with Matching Styles
* Click an image to visit the corresponding website.
Sample Companion Websites for Scientific Publications
* Click an image to visit the corresponding website.
Medicago Protein Database
Plant Physiol. 2010, 152(1): 19-28.
The data presented here represents a large-scale shotgun mass spectrometry analysis of peptides derived from Medicago root proteins.
Genome Res. 2008, 18(5): 706-16.
This database allows you to search gene expression in 6 key tissues as a function of obesity, strain, and age, in a mouse model of type II diabetes.
MitoMod Protein Database
Cell Metab. 2012, 16(5): 672-83
MitoMod serves as a resource for investigating the levels of site-specific phosphorylation on mitochondrial proteins.
Sample Business Websites With Integrated E-Commerce Solutions
* Click an image to visit the corresponding website.
Scientific Lab Info Systems
At BioInfoRx, we specialize in tailor-made scientific information system development services. Our focus is on delivering web-based solutions that are dependable, built on our exclusive BxAF application framework technologies.
Over the years, we have designed and developed several sophisticated data management and processing systems for a wide range of clients, including individual labs, core facilities, small biotech businesses, and large pharmaceutical companies. Our expertise covers various fields, including genomics, proteomics, metabolomics, and custom applications.
Tailored Tracking Solutions for Diverse Clientele
As a provider of custom item and sample tracking systems, we cater to the unique needs of our diverse clientele. We understand that every customer has their own requirements, and we work closely with them to develop tailored solutions that meet their specific demands.
Our expertise and experience allow us to create customized systems that can handle various types of items and samples, regardless of their size or quantity. We take into account the entire process, from the time an item is received until it is dispatched, ensuring that our clients have complete visibility and control over their inventory.
Our commitment to delivering high-quality systems has earned us the trust and loyalty of our customers. We continue to refine and improve our offerings to stay ahead of the curve and provide the best possible solutions to meet their evolving needs.
The LIMS for a research lab to track all items in the lab.
The LIMS to manage everything in an office.
The LIMS for a public diagnostic company to track samples and DNA extraction process.
The LIMS tracks blood, stool, and tissue samples. It comes with automated tools for sample extraction, dilution calculation, etc. Multiple users can access the system at the same time, but with different roles.
This LIMS was used by company with thousands of samples and boxes. Visual storage hierarchy structure and drag-and-drop sample relocation allow the company to organize everything.
This LIMS was used by a virus discovery facility to track patient sample information and automate the discovery process. It can track very complicated information as indicated by the long menu.
Complex LIMS for Metabolomics-Based Biomarker Discovery
American Society for Mass Spectrometry, June 2009.
A Laboratory Information Management System (LIMS) for High-Throughput LC-MS Metabolomics-Based Biomarker Discovery
The LIMS system combines experiments, samples, LC-MS, feature analysis, and interpretation of data into an interconnected web-based user interface:
- System designed to handle thousands of LC-MS samples from planning to final interpretation
- Open source framework allows rapid integration of new project specific data analysis tools
- Complex analysis procedures were simplified into simple web-based interfaces allowing virtually complete automation of data analysis procedures
The user-friendly interfaces of our platform enable the processing of open source mass spectrometry-based data formats, such as NetCDF/mzXML. Our preprocessing pipelines provide access to an extensive array of peak picking and alignment algorithms. Additionally, our flexible analysis pipeline empowers users to conduct cutting-edge statistical and chemometric analysis of mass feature abundances. This includes ANOVAs, t-tests, principle component analysis and machine learning techniques.
This LIMS was for a metabolomic start-up company to manage entire business processes. This is a general overview of analysis pipeline combining proprietary and open source software.
The easy-to-use interfaces allow users to process open source mass spectrometry-based data formats including NetCDF/mzXML. The preprocessing pipelines give users access to a wide range of peak picking and alignment algorithms.
(Left) LIMS interface for Developmental Toxicity metabolomics platform. A large number of tools are available for the user to manage and analyze data.
(Right) LIMS generates plots based on the results of summary information, univariate, and multivariate statistics.
Systems for DNA Oligo Synthesis Companies
This comprehensive system handles information throughout the entire process, from customer orders placed through e-commerce to internal order processing, oligo synthesis, product labeling and packing slip creation, invoice generation, product delivery, and information review and updating. One of its key features is bioinformatics integration, which enables the system to calculate all necessary DNA/RNA oligo properties, including MW, Tm, Eps, and more. Additionally, the system boasts an extensive pricing system that can handle complex pricing scenarios, such as price per base, special discounts, individual pricing for purification, modification, and beyond.
Enter Orders
Submit Orders
Search Oligos
LIMS for Molecular Biological Laboratories
- The system offers centralized storage, access control, and system configuration, allowing for easy updates and management.
- With world-wide access and an intuitive user interface, users can access the system from anywhere and use it with ease.
- Bioinformatics integration is included, allowing for seamless integration with other bioinformatics tools and databases.
- Electronic lab notebooks are available, making it easy to keep track of experiments and data.
- Instant result reports and dynamic project progress reports are provided, allowing for quick and easy monitoring of ongoing projects.
- The system promotes forward information flow, ensuring that information is shared efficiently between team members.
- SQL is used for universal database connection and data exchange, allowing for easy integration with other databases and tools.
- Multi-level control of security is implemented, with automatic daily backup to ensure data safety and security.
- The system is cost-effective, taking advantage of "free" resources to minimize costs and maximize value.
Project information management system
- File Sharing:
- Secure document sharing for group members
- Tools for directory and file manipulation (create, upload/download, delete, copy, move, search)
- Tree-view of directories and files
- Online File Storing:
- Secure online file storage for file owners
- Tools for directory and file manipulation (create, upload/download, delete, copy, move, search)
- Tree-view of directories and files
- Group E-mails:
- WYSIWYG interface for composing HTML messages
- Capability to attach multiple files
- Connection to database for saving e-mails in database instead of on server
- Composer connected to database for sending group e-mails, attaching client and server side files, and integration with other tools
- Public Discussion Forum:
- Enables online discussion of topics
- All posted messages can be reviewed at any time with internet connection
- Search tool for finding previously posted messages
- Private Group Discussion Forum:
- Enables online discussion of topics among selected group members
- All posted messages can be reviewed at any time with internet connection
- Search tool for finding previously posted messages
- Group-based Daily Task Management:
- Enables managing daily tasks for assigners and assignees
- Assigners can create tasks for assignees, who can add follow-ups, update status, or delegate tasks to others
- Both assigners and assignees can review tasks in real time, with overdue tasks highlighted
- File attachments allowed, with automated e-mails sent for task status changes
- Group-based Announcements and Events:
- A platform for posting announcements and group events
- Readers can post follow-ups
- Private Daily Notes:
- Diary-like tool for recording daily notes
- Only owner can review notes
Workflow Automation
BioInfoRx helps research labs and biotech companies to optimize their workflow, digitalize information, and automate workflow as much as possible through innovative web-based systems.
- Proven technologies guarantee reliable, expandable, and flexible solutions.
- We understand customers' needs and deliver rapid solutions.
- Cost effective due to cloud-based solutions, extensive experience, and mature technologies.
Automation of Antibody Production Process
The LIMS system is essential for the business, it covers:
- Customer information tracking
- Workorder generation and tracking
- Project initiation, progress, and all daily task information
- Daily tasks for employees in each step
- Automated workflow for many steps, e.g., ELISA data plots, clone picking, etc.
The system converts complicated workflow and hard-copy of records to fully digital and clearly defined workflow. It also automates workflow in numerous steps.
(Left) LIMS interface for Developmental Toxicity metabolomics platform. A large number of tools are available for the user to manage and analyze data.
(Right) LIMS generates plots based on the results of summary information, univariate, and multivariate statistics.
Automation of Business Process for Biotech Service Company
The system automates the business process for DNA sequencing companies or facilities. The following steps are automated and linked in the system.
- Customer creates account
- Customer submits samples information online
- Technician receives samples, update status online and an email will be send to the customer
- Samples, reagents, enzymes, and plates are tracked by an inventory system.
- System creates plat layout to load samples to sequencer
- System automatically separates data from 96-well plates according to customers, and upload data to individual customer’s folder.
- Customer received notification and can download data online
- Invoice was created and emailed to Customer, payment status is tracked.
- Importing oligo information from third-party software outputs
- Automated generation of key information based on bioinformatic computation
- Integrated ordering systems
- Integrated item tracking and space allocation
- Powerful search integrated with bioinformatic algorithms
- Role-based access control of systems
Automation of Transgenic Animal Production
BioInfoRx has built transgenic animal workflow management systems for multiple core facilities and large animal research centers. The workflow steps can be customized according to each facility’s unique needs. The system can be used as standalone system, or can be integrated with mLIMS.
Big Data Processing
BioInfoRx has a long history of supporting big data analysis and visualization for research labs, covering gene sequences, genomics, proteomics, metabolomics, and other specialized fields. Here are some related publications:
- EzArray: A web-based highly automated Affymetrix expression array data management and analysis system. BMC Bioinformatics 2008, 9:46
- A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Res. 2008, 18(5): 706-16.
- Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes. Plant Physiol. 2010, 152(1): 19-28.
- A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis. Cell Metab. 2012, 16(5): 672-83
Complex Information System for a Diabetes Research Lab
Keller et al, Genome Research, 18:706-716, 2008
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
The LIMS system contains many tools for lab management and data analysis in one interconnected web-based user interface.
- Management of large research files
- Powerful research tools covering time course data, genomic information, metabolite levels, miRNA tools, cross-species comparative mapping and so on.
- Integration with publications, allowing users to search through the database for interested genes.
The LIMS system contains many tools for lab management and data analysis. For example, powerful search tool for time course data, Power search tool for time course data - Electronic Northerns, Search correlated transcripts for any transcript, Check correlation between any two transcripts, Search correlated transcripts with miRNA copy numbers, Liver metabolite levels in time course animals, and so on. It also has tools for laboratory Mice, and more.
A gene-gene network model is distinct between B6 and BTBR mice. A gene-gene network was constructed based on the partial correlation (PaCor) between the strain-specific PC1 calculated between all modules identified in the 6 tissues profiled.
Graphically display of gene expression data from 60 arrays / 12 conditions. The system allows researchers to search, plot, and compare expression level through multiple array experiment results.
MitoMod: A compilation of dynamic mitochondrial protein phosphosites
Cell Metab. 2012, 16(5): 672-83
A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis.
MitoMod serves as a resource for investigating the levels of site-specific phosphorylation on mitochondrial proteins. This data was compiled using multiplexed quantitative mass spectrometry of liver mitochondria from more than 50 mice during both acute and chronic physiological transformations.
Analysis and Visualization of Behavioral Testing Results
Fly sleep behavior was assayed using the Drosophila Activity Monitoring System. The data collected was processed and displayed online.
