Custom Web Systems

BioInfoRx offer a variety of cloud-based systems for scientific research.

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 Metabolomics Based Biomarker Discovery
  • Systems for DNA Oligo Synthesis Companies
  • LIMS for Molecular Biological Laboratories
  • Project information management system

Workflow Automation

  • Automation of Antibody Production Process
  • Automation of Business Process for Biotech Service Company
  • Automation of Transgenic Animal Production

Big Data Processing

  • Complex Information System for a Diabetes Research Lab
  • MitoMod: A compilation of dynamic mitochondrial protein phosphosites
  • Analysis and Visualization of Behavioral Testing Results

Websites & Intranets

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BioInfoRx offers website development services to academic and business 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

Research Lab Websites with Matching Styles

* Click an image to visit the corresponding website.

Xu Lab, UW-Madison

Ge Lab, UW-Madison

Clarke Labs, Georgetown U.

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.

Diabetes Database
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.

Business Websites With Integrated E-Commerce Solutions

* Click an image to visit the corresponding website.

Oblique Bio, Inc.

BioTrand, Inc.

Functional Biosciences

Scientific Lab Info Systems

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BioInfoRx provides custom scientific information system development services. We deliver reliable web-based solutions based on our proprietary application framework technologies, BxAF™.

We have built numerous advanced data management and processing systems for individual labs, core facilities, small biotech businesses, and large pharmaceutical companies, covering genomics, proteomics, metabolomics, and custom fields.

Custom Item and Sample Tracking Systems for Different Customers

BioInfoRx sample tracking systems are widely used and have been customized in various ways to meet customers' special needs. Our customers include regular research labs, core facilities, biotech and pharma companies, and even non-scientific organizations (e.g., high schools, restaurants, etc.).

The LIMS for a research lab to track all items in the lab, from office supplies, desktop items, freezer items, items in every drawer. It features drag-and-drop image uploading, auto-linking to Youtube videos, using barcode and mobile devices to relocate items, and so on.

Everything in the office has been recorded.

The LIMS was developed 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.

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 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. A flexible analysis pipeline was created to allow users to perform state-of-the-art statistical and chemometric analysis of the mass feature abundances, including ANOVAs, t-tests, principle component analysis and machine learning techniques.

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 system manages information from all steps in the process, including customer ordering (e-commerce), internal order processing, oligo synthesis, printing product labels and packing slips, generating invoices, product delivery, and information reviewing and updating.
  • An important feature of the system is bioinformatics integration. The system calculates all required properties of the DNA/RNA oligos (e.g. MW, Tm, Eps and so on).
  • The system comes with a comprehensive pricing system that takes care of complicated situations, such as price per base, special discount, individual pricing for purification, modification, and so on.

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Search Oligos

LIMS for Molecular Biological Laboratories

  • Centralized storage, update, access control, and system configuration
  • World-wide access and intuitive user interface
  • Bioinformatics integration
  • Electronic lab notebooks
  • nstant result reports and dynamic project progress reports
  • Forward information flow
  • SQL: universal database connection and data exchange
  • Multi-level control of security and automatic daily backup
  • Cost-effective: taking advantage of the "free" resources

Project information management system

  • File Sharing. This tool solves the problem of sharing documents with high security. Only group members can access your shared files; nevertheless, they cannot modify your shared files. It provides tools to manipulate directories and files (create, upload and download, delete, copy, move, and search). In addition, this module provides tree-view of directories and files.
  • Online File Storing. This tool saves files online with high security. Only file owners can access their files. It provides tools to manipulate directories and files (create, upload and download, delete, copy, move, and search). In addition, this module provides tree-view of directories and files.
  • Group e-mails. WYSIWYG interface to compose HTML messages, capability to attach multiple files, and connection to database, allowing saving e-mails in database instead of on server. The composer is connected to database, allowing to send group e-mails, attach both client and server side files, and integrated with other tools.
  • Public Discussion Forum. This tool enables users to discuss certain topics online instead of sending e-mails back and forth. All posted messages can be reviewed at any time anywhere with internet connection. A search tool provides great convenience to find previously posted messages.
  • Private Group Discussion Forum. This tool enables users to discuss certain topics online among selected group members instead of sending e-mails back and forth. All posted messages can be reviewed at any time anywhere with internet connection. A search tool provides great convenience to find previously posted messages.
  • Group-based Daily Task Management. This tool enables managing daily tasks. Registered users (assigners) can create new tasks for others (assignee). Assignee can add follow-ups to the tasks, update the task status, or delegate the task to others. The assigner can also re-assign the task to others. Both assigners and assignee will be able to review the tasks in real time. The task passed due time will be highlighted. File attachments are allowed. Automated e-mails will be sent out whenever task status has been changed.
  • Group-based Announcements and Events. A good place to post announcements and group events. Readers can post follow-ups.
  • Private Daily Notes. This tool provides "diary"-like functions for users to record their daily notes. Only the owner can review the notes.

Workflow Automation

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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

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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:

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.