Write a JOSS submission

docs/paper/code/figures.py

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+"""Generate figures for paper.md
+"""
+
+from shapeflow.config import loads
+from shapeflow.video import init
+
+
+if __name__ == '__main__':
+    # Example figure: SIMPLE-iSIMPLE shuttle
+    va = init(loads("../assets/shuttle.json"))
+
+    va.analyze()
+

docs/paper/paper.bib

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+@article{Mohammed:2015,
+title = "Lab-on-a-chip or Chip-in-a-lab: Challenges of Commercialization Lost in Translation",
+journal = "Procedia Technology",
+volume = "20",
+pages = "54 - 59",
+year = "2015",
+note = "Proceedings of The 1st International Design Technology Conference, DESTECH2015, Geelong",
+issn = "2212-0173",
+doi = "https://doi.org/10.1016/j.protcy.2015.07.010",
+url = "http://www.sciencedirect.com/science/article/pii/S2212017315001875",
+eprint = "http://www.sciencedirect.com/science/article/pii/S2212017315001875",
+author = "Mazher Iqbal Mohammed and Steven Haswell and Ian Gibson",
+keywords = "lab-on-a-chip, commercialization, microfluidics, translation",
+abstract = "Lab-on-a-chip technology has been long envisaged to have tremendous commercial potential, owing to the ability of such devices to encapsulate a full range of laboratory processes in a single instrument and operate in a portable manner, rapidly and at low cost. Devices are believed to have potential in fields ranging across medical diagnostics, environmental sampling and a range of consumer products, however, to date very few devices have attained commercial success. This review examines the challenges relating to the commercialization of lab-on-a-chip technology from fundamental research to mass manufacturing and aims to provide insight to both academics and product development specialists the perceived hindrances to commercialization and a strategy by which future work could be translated into commercial success."
+}
+
+@article{Martinez:2010,
+author = "Martinez, Andres W. and Phillips, Scott T. and Whitesides, George M. and Carrilho, Emanuel",
+title = "Diagnostics for the Developing World: Microfluidic Paper-Based Analytical Devices",
+journal = "Analytical Chemistry",
+volume = "82",
+number = "1",
+pages = "3-10",
+year = "2010",
+doi = "https://doi.org/10.1021/ac9013989",
+note ="PMID: 20000334",
+url = "https://doi.org/10.1021/ac9013989",
+eprint = "https://doi.org/10.1021/ac9013989"
+}
+
+@article{Eltzov:2015,
+author = "Eltzov, Evgeni and Guttel, Sarah and Low Yuen Kei, Adarina and Sinawang, Prima Dewi and Ionescu, Rodica E. and Marks, Robert S.",
+title = "Lateral Flow Immunoassays – from Paper Strip to Smartphone Technology",
+journal = "Electroanalysis",
+volume = "27",
+number = "9",
+pages = "2116-2130",
+keywords = "Lateral flow immunoassays, Paper strip, Smartphone biosensors",
+doi = "https://doi.org/10.1002/elan.201500237",
+url = "https://onlinelibrary.wiley.com/doi/abs/10.1002/elan.201500237",
+eprint = "https://onlinelibrary.wiley.com/doi/pdf/10.1002/elan.201500237",
+abstract = "Abstract Lateral flow immunoassays provide low cost, fast, portable and simple to use devices, with yes/no answers seen by the naked eye, that has found applications in agriculture, biomedicine, the environment, and food industries. Making these quantitative, via electrochemical or optical approaches, is the present day challenge, with a vision that one day, these will be connected to smartphone technologies, which exhibit a promising digital platform for point-of-care diagnostics, mobile healthcare and bioanalytical needs. These devices are fully automated and equipped with a high resolution camera, a powerful processor with high storage capacity, wireless connectivity, real-time geo-tagging, secure data management, and cloud computing.",
+year = "2015"
+}
+
+@Article{Kokalj:2014,
+author = "Kokalj, Tadej and Park, Younggeun and Vencelj, Matjaž and Jenko, Monika and Lee, Luke P.",
+title = "Self-powered Imbibing Microfluidic Pump by Liquid Encapsulation: SIMPLE",
+journal = "Lab Chip",
+year = "2014",
+volume = "14",
+issue = "22",
+pages = "4329-4333",
+publisher = "The Royal Society of Chemistry",
+doi = "https://doi.org/10.1039/C4LC00920G",
+url = "http://dx.doi.org/10.1039/C4LC00920G",
+abstract = "Reliable, autonomous, internally self-powered microfluidic pumps are in critical demand for rapid point-of-care (POC) devices, integrated molecular-diagnostic platforms, and drug delivery systems. Here we report on a Self-powered Imbibing Microfluidic Pump by Liquid Encapsulation (SIMPLE), which is disposable, autonomous, easy to use and fabricate, robust, and cost efficient, as a solution for self-powered microfluidic POC devices. The imbibition pump introduces the working liquid which is sucked into a porous material (paper) upon activation. The suction of the working liquid creates a reduced pressure in the analytical channel and induces the sequential sample flow into the microfluidic circuits. It requires no external power or control and can be simply activated by a fingertip press. The flow rate can be programmed by defining the shape of utilized porous material: by using three different paper shapes with circular section angles 20°, 40° and 60°, three different volume flow rates of 0.07 μL s−1, 0.12 μL s−1 and 0.17 μL s−1 are demonstrated at 200 μm × 600 μm channel cross-section. We established the SIMPLE pumping of 17 μL of sample; however, the sample volume can be increased to several hundreds of μL. To demonstrate the design, fabrication, and characterization of SIMPLE, we used a simple, robust and cheap foil-laminating fabrication technique. The SIMPLE can be integrated into hydrophilic or hydrophobic materials-based microfluidic POC devices. Since it is also applicable to large-scale manufacturing processes, we anticipate that a new chapter of a cost effective, disposable, autonomous POC diagnostic chip is addressed with this technical innovation."
+}
+
+@Article{DalDosso:2018,
+author="Dal Dosso, Francesco and Kokalj, Tadej and Belotserkovsky, Jaroslav and Spasic, Dragana and Lammertyn, Jeroen",
+title="Self-powered infusion microfluidic pump for ex vivo drug delivery",
+journal="Biomedical Microdevices",
+year="2018",
+month="May",
+day="31",
+volume="20",
+number="2",
+pages="44",
+abstract="In this work, we present a new iSIMPLE concept (infusion Self-powered Imbibing Microfluidic Pump by Liquid Encapsulation), which requires no external power for activation nor liquid manipulation, it is easy to use while its fabrication method is extremely simple, inexpensive and suited for mass replication. The pump consists of a working liquid, which is - after finger activation - absorbed in a porous material (e.g. filter paper). The air expelled from the porous material increases the pressure in the downstream outlet channel and propels the outlet liquid (i.e. the sample) through the channel or ejects it. Here we investigated the influence of different filter papers on the iSIMPLE flow rates, achieving a wide range from 30 down to 0.07 $\mu$L/min. We also demonstrated the versatility of the iSIMPLE in terms of the liquid volume that can be manipulated (from 0.5 $\mu$L up to 150 $\mu$L) and the working pressure reaching 64 kPa, unprecedented high for a self-powered microfluidics pump. In addition, using a 34 G microneedle mounted on the iSIMPLE, we successfully injected liquids with different viscosities (from 0.93 up to 55.88 cP) both into an agarose matrix and a skin-like biological ex vivo substrate (i.e. chicken breast tissue). This work validated the compatibility of the iSIMPLE with drug delivery in a controlled way into a skin-like matrix, envisioning a whole new scenario for intradermal injections using self-contained skin patch. In addition, due to the extreme flexibility of the design and manufacturing, the iSIMPLE concept offers enormous opportunities for completely autonomous, portable and cost effective LOC devices.",
+issn="1572-8781",
+doi="10.1007/s10544-018-0289-1",
+url="https://doi.org/10.1007/s10544-018-0289-1"
+}
+
+@article{DalDosso:2019,
+title = "SIMPLE analytical model for smart microfluidic chip design",
+journal = "Sensors and Actuators A: Physical",
+volume = "287",
+pages = "131 - 137",
+year = "2019",
+issn = "0924-4247",
+doi = "https://doi.org/10.1016/j.sna.2019.01.005",
+url = "http://www.sciencedirect.com/science/article/pii/S0924424718318910",
+author = "Dal Dosso, Francesco and Bondarenko,Yura and Kokalj, Tadej and Lammertyn, Jeroen",
+keywords = "Self-powered microfluidics, analytical model, flow-rate design tool, SIMPLE pump",
+abstract = "Precise control of the flow dynamics in a microfluidic device is of great importance for the integration of bioassays on-chip. Recently, the Self-powered Imbibing Microfluidic Pump by Liquid Encapsulation (SIMPLE) was developed in our group and integrated with biological applications. The system functions based on capillary imbibition of a working liquid (WL) into a porous material (PM), which in turn pulls a sample liquid (SL) through the connected microfluidic channel network. Analytical models describing the pumping dynamics of paper-based and channel-based systems have been presented, but no suitable analytical models have been reported for hybrid systems such as SIMPLE. Moreover, the available models were mostly limited to only describing the pumping process (i.e. flow rate) for given design parameters (i.e. paper shape, channels geometry), which still resulted in tedious trial-and-error process to optimize the chip design to achieve the desired flow rate. In this work, we developed a smart designing tool for SIMPLE-based chips that provides the design parameters necessary to obtain a targeted flow rate. An analytical model for the SIMPLE was first derived and validated, confirming its 3 main hypotheses: i) the sample flow rate is dependent on the porous material geometry but independent from the ii) porous material volume and iii) channel geometry. All experimental results were in good agreement with this model. Finally, we used our model as a prediction tool providing precise design parameters to avoid the time-consuming trial-and-error approach needed to achieve a specific flow rate. In particular, several chips were fabricated according to the model inputs and the sample liquid flow rates measured (1.5 ± 0.3, 5.3 ± 1.5, 15.2 ± 2.7 μL/min) were matching the targeted ones (1.5, 5, 15 μL/min). The analytical model developed in this work was proven to be a useful designing tool for fast and efficient optimization of SIMPLE-based chips in order to address specific application requirements."
+}
+
+@article{Hu:2014,
+title = "Advances in paper-based point-of-care diagnostics",
+journal = "Biosensors and Bioelectronics",
+volume = "54",
+pages = "585 - 597",
+year = "2014",
+issn = "0956-5663",
+doi = "https://doi.org/10.1016/j.bios.2013.10.075",
+url = "http://www.sciencedirect.com/science/article/pii/S095656631300777X",
+author = "Jie Hu and ShuQi Wang and Lin Wang and Fei Li and Belinda Pingguan-Murphy and Tian Jian Lu and Feng Xu",
+keywords = "Microfluidics, Point-of-care (POC), Paper-based diagnostics",
+abstract = "Advanced diagnostic technologies, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA), have been widely used in well-equipped laboratories. However, they are not affordable or accessible in resource-limited settings due to the lack of basic infrastructure and/or trained operators. Paper-based diagnostic technologies are affordable, user-friendly, rapid, robust, and scalable for manufacturing, thus holding great potential to deliver point-of-care (POC) diagnostics to resource-limited settings. In this review, we present the working principles and reaction mechanism of paper-based diagnostics, including dipstick assays, lateral flow assays (LFAs), and microfluidic paper-based analytical devices (μPADs), as well as the selection of substrates and fabrication methods. Further, we report the advances in improving detection sensitivity, quantification readout, procedure simplification and multi-functionalization of paper-based diagnostics, and discuss the disadvantages of paper-based diagnostics. We envision that miniaturized and integrated paper-based diagnostic devices with the sample-in-answer-out capability will meet the diverse requirements for diagnosis and treatment monitoring at the POC."
+}
+