Automating functional enzyme screening & characterization

This work has been presented in the 10th IWBDA workshop.Microfluidics continue to gain traction as an inexpensive alternative to standard multi-well plate-based, and flow cytometry- based, assay platforms. These devices are especially useful for the types of ultra-high throughput screens needed for enzyme discovery applications where large numbers (>106) of unique samples must be screened rapidly1. Coupled with cell-free protein synthesis2, microfluidics are being used to identify novel enzymes useful for a variety of applications with unprecedented speed. However, these devices are typically produced using PDMS, and require considerable infrastructure and artisanal skill to fabricate, limiting their accessibility. Likewise, enzyme hits obtained from a screen are often validated manually and would benefit from automation of downstream validation processes. To address these limitations, we propose a workflow which leverages software tools to automate the rapid design and fabrication of low-cost polycarbonate microfluidic devices for use as high-throughput screening platforms for enzyme discovery, as well as an automated DNA assembly tool to streamline validation of screening candidates. Using this workflow, we aim to identify novel oxidoreductase enzymes from environmental metagenomic DNA libraries, for use in electrochemical biosensors

A reverse predictive model towards design automation of microfluidic droplet generators

This work has been presented in the 10th IWBDA workshop.Droplet-based microfluidic devices in comparison to test tubes can reduce reaction volumes 10^9 times and more due to the encapsulation of reactions in micro-scale droplets [4]. This volume reduction, alongside higher accuracy, higher sensitivity and faster reaction time made droplet microfluidics a superior platform particularly in biology, biomedical, and chemical engineering. However, a high barrier of entry prevents most of life science laboratories to exploit the advantages of microfluidics. There are two main obstacles to the widespread adoption of microfluidics, high fabrication costs, and lack of design automation tools. Recently, low-cost fabrication methods have reduced the cost of fabrication significantly [7]. Still, even with a low-cost fabrication method, due to lack of automation tools, life science research groups are still reliant on a microfluidic expert to develop any new microfluidic device [3, 5]. In this work, we report a framework to develop reverse predictive models that can accurately automate the design process of microfluidic droplet generators. This model takes prescribed performance metrics of droplet generators as the input and provides the geometry of the microfluidic device and the fluid and flow settings that result in the desired performance. We hope this automation tool makes droplet-based microfluidics more accessible, by reducing the time, cost, and knowledge needed for developing a microfluidic droplet generator that meets certain performance requirement

Design automation based on fluid dynamics

This article was accepted and presented at the 9th International Workshop on Bio-Design Automation, Pittsburgh, Pennsylvania (2017).Microfluidic devices provide researchers with numerous advantages such as high throughput, increased sensitivity and accuracy, lower cost, and reduced reaction time. However, design, fabrication, and running a microfluidic device are still heavily reliant on expertise. Recent studies suggest micro-milling can be a semi-automatic, inexpensive, and simple alternative to common fabrication methods. Micro-milling does not require a clean-room, mask aligner, spin-coater, and Plasma bonder, thus cutting down the cost and time of fabrication significantly. Moreover, through this protocol researchers can easily fabricate microfluidic devices in an automated fashion eschewing levels of expertise required for typical fabrication methods, such as photolithography, soft-lithography, and etching. However, designing a microfluidic chip that meets a certain set of requirements is still heavily dependent on a microfluidic expert, several days of simulation, and numerous experiments to reach the required performance. To address this, studies have reported random automated design of microfluidic devices based on numerical simulations for micro-mixing. However, random design generation is heavily reliant on time-consuming simulations carried out beforehand, and is prone to error due to the accuracy limitations of the numerical method. On the other hand, by using micro-milling for ultra-fast and inexpensive fabrication of microfluidic devices and Taguchi design of experiments for state-space exploration of all of the geometric parameters, we are able to generate a database of geometries, flow rates, and flow properties required for a single primitive to carry out a specified microfluidic task

Web Application Reinforcement via Efficient Systematic Analysis and Runtime Validation (ESARV)

Securing the data, a fundamental asset in an organization, against SQL Injection (SQLI), the most frequent attack in web applications, is vital. In SQLI, an attacker alters the structure of the actual query by injecting code via the input, and gaining access to the database. This paper proposes a new method for securing web applications against SQLI Attacks (SQLIAs). It contains two phases based on systematic analysis and runtime validation and uses our new technique for detection and prevention. At the static phase, our method removes user inputs from SQL queries and gathers as much information as possible, from static and dynamic queries in order to minimize the overhead at runtime. On the other hand, at the dynamic phase, the prepared information alongside our technique are used to check the validity of the runtime query. To facilitate the usage of our method and show our expectations in practice, ESARV was implemented. The empirical evaluations demonstrated in this paper, indicate that ESARV is efficient, accurate, effective, and also has no deployment requirements

Geoelectrical investigation for the assessment of groundwater conditions: a case study

An electrical resistivity survey involving Vertical Electrical Soundings (VES) was carried out in the Shooro Basin in Southeast Iran in order to study groundwater conditions such as depth, thickness and aquifer boundaries. Vertical electrical soundings by Schlumberger array were conducted in this area. The resistivity Schlumberger soundings which have a maximum current electrode spacing (AB) ranging from 200 m to 600 m were carried out at 207 positions in 19 profiles. Interpretation of these soundings indicates the presence of an alluvial aquifer. This aquifer is divided into eastern and western parts by the Shooro River, which comprises a variable thickness and resistivity of deposits. The average permeability coefficient and resistivity in the western part, especially southwest is higher than the eastern part of the aquifer. Therefore, it seems that Shooro River follows a fault zone in the region. The high resistivity of west part is due to the water quality and the existence of alluvial fan with coarse grain materials. Low aquifer resistivities in the east are associated with finer materials and also brackish water infiltration from the adjacent basin mainly in the central part of the aquifer. Furthermore, zones with high yield potential have been determined in this research based on the resistivity data