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Jiang S, Evans-Yamamoto D, Bersenev D, Palaniappan SK, Yachie-Kinoshita A. ProtoCode: Leveraging large language models (LLMs) for automated generation of machine-readable PCR protocols from scientific publications. SLAS Technol 2024; 29:100134. [PMID: 38670311 DOI: 10.1016/j.slast.2024.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Protocol standardization and sharing are crucial for reproducibility in life sciences. In spite of numerous efforts for standardized protocol description, adherence to these standards in literature remains largely inconsistent. Curation of protocols are especially challenging due to the labor intensive process, requiring expert domain knowledge of each experimental procedure. Recent advancements in Large Language Models (LLMs) offer a promising solution to interpret and curate knowledge from complex scientific literature. In this work, we develop ProtoCode, a tool leveraging fine-tune LLMs to curate protocols into intermediate representation formats which can be interpretable by both human and machine interfaces. Our proof-of-concept, focused on polymerase chain reaction (PCR) protocols, retrieves information from PCR protocols at an accuracy ranging 69-100 % depending on the information content. In all tested protocols, we demonstrate that ProtoCode successfully converts literature-based protocols into correct operational files for multiple thermal cycler systems. In conclusion, ProtoCode can alleviate labor intensive curation and standardization of life science protocols to enhance research reproducibility by providing a reliable, automated means to process and standardize protocols. ProtoCode is freely available as a web server at https://curation.taxila.io/ProtoCode/.
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Affiliation(s)
- Shuo Jiang
- SBX BioSciences, Inc. 1600 - 925 West Georgia Street, Vancouver, BC, V6C 3L2, Canada
| | - Daniel Evans-Yamamoto
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Dennis Bersenev
- SBX BioSciences, Inc. 1600 - 925 West Georgia Street, Vancouver, BC, V6C 3L2, Canada
| | - Sucheendra K Palaniappan
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan.
| | - Ayako Yachie-Kinoshita
- SBX BioSciences, Inc. 1600 - 925 West Georgia Street, Vancouver, BC, V6C 3L2, Canada; The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan.
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2
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The Role of Process Systems Engineering in Applying Quality by Design (QbD) in Mesenchymal Stem Cell Production. Comput Chem Eng 2023. [DOI: 10.1016/j.compchemeng.2023.108144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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3
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Li J, Liu L, Zhang J, Qu X, Kawamura T, Miyagawa S, Sawa Y. Engineered Tissue for Cardiac Regeneration: Current Status and Future Perspectives. Bioengineering (Basel) 2022; 9:605. [PMID: 36354516 PMCID: PMC9688015 DOI: 10.3390/bioengineering9110605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2023] Open
Abstract
Heart failure (HF) is the leading cause of death worldwide. The most effective HF treatment is heart transplantation, the use of which is restricted by the limited supply of donor hearts. The human pluripotent stem cell (hPSC), including human embryonic stem cell (hESC) and the induced pluripotent stem cells (hiPSC), could be produced in an infinite manner and differentiated into cardiomyocytes (CMs) with high efficiency. The hPSC-CMs have, thus, offered a promising alternative for heart transplant. In this review, we introduce the tissue-engineering technologies for hPSC-CM, including the materials for cell culture and tissue formation, and the delivery means into the heart. The most recent progress in clinical application of hPSC-CMs is also introduced. In addition, the bottleneck limitations and future perspectives for clinical translation are further discussed.
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Affiliation(s)
- Junjun Li
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Li Liu
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Jingbo Zhang
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Xiang Qu
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Takuji Kawamura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yoshiki Sawa
- Cardiovascular Division, Osaka Police Hospital, Tennoji, Osaka 543-0035, Japan
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4
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Kanda GN, Tsuzuki T, Terada M, Sakai N, Motozawa N, Masuda T, Nishida M, Watanabe CT, Higashi T, Horiguchi SA, Kudo T, Kamei M, Sunagawa GA, Matsukuma K, Sakurada T, Ozawa Y, Takahashi M, Takahashi K, Natsume T. Robotic search for optimal cell culture in regenerative medicine. eLife 2022; 11:77007. [PMID: 35762203 PMCID: PMC9239686 DOI: 10.7554/elife.77007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/17/2022] [Indexed: 12/25/2022] Open
Abstract
Induced differentiation is one of the most experience- and skill-dependent experimental processes in regenerative medicine, and establishing optimal conditions often takes years. We developed a robotic AI system with a batch Bayesian optimization algorithm that autonomously induces the differentiation of induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells. From 200 million possible parameter combinations, the system performed cell culture in 143 different conditions in 111 days, resulting in 88% better iPSC-RPE production than that obtained by the pre-optimized culture in terms of the pigmentation scores. Our work demonstrates that the use of autonomous robotic AI systems drastically accelerates systematic and unbiased exploration of experimental search space, suggesting immense use in medicine and research.
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Affiliation(s)
- Genki N Kanda
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Robotic Biology Institute Inc., Tokyo, Japan
| | | | - Motoki Terada
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,VCCT Inc., Kobe, Japan
| | - Noriko Sakai
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,VCCT Inc., Kobe, Japan
| | - Naohiro Motozawa
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Tomohiro Masuda
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,VCCT Inc., Kobe, Japan
| | - Mitsuhiro Nishida
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,VCCT Inc., Kobe, Japan
| | | | | | | | - Taku Kudo
- Robotic Biology Institute Inc., Tokyo, Japan
| | | | - Genshiro A Sunagawa
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory for Molecular Biology of Aging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | | | | | - Masayo Takahashi
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,VCCT Inc., Kobe, Japan.,Vision Care Inc., Kobe, Japan
| | - Koichi Takahashi
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tohru Natsume
- Robotic Biology Institute Inc., Tokyo, Japan.,Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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5
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Liu AW, Villar-Briones A, Luscombe NM, Plessy C. Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing. F1000Res 2022; 11:240. [PMID: 35350547 PMCID: PMC8931447 DOI: 10.12688/f1000research.109251.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Automation has increasingly become more commonplace in the research laboratory workspace. The introduction of articulated robotic arms allows the researcher more flexibility in the tasks a single piece of automated machinery can perform. We set out to incorporate automation in processing of genomic DNA organic extractions to increase throughput and limit researchers to the exposure of organic solvents. Methods: In order to automate the genome sequencing pipeline in our laboratory, we programmed a dual-arm anthropomorphic robot, the Robotic Biology Institute's Maholo LabDroid, to perform organic solvent-based genomic DNA extraction from cell lysates. To the best of our knowledge, this is the first time that automation of phenol-chloroform extraction has been reported. Results:
We achieved routine extraction of high molecular weight genomic DNA (>100 kb) from diverse biological samples including algae cultured in sea water, bacteria, whole insects, and human cell lines. The results of pulse-field electrophoresis size analysis and the N50 sequencing metrics of reads obtained from Nanopore MinION runs verified the presence of intact DNA suitable for direct sequencing. Conclusions: We present the workflow that can be used to program similar robots and discuss the problems and solutions we encountered in developing the workflow. The protocol can be adapted to analogous methods such as RNA extraction, and there is ongoing work to incorporate further post-extraction steps such as library construction. This work shows the potential for automated robotic workflows to free molecular biological researchers from manual interventions in routine experimental work. A time-lapse movie of the entire automated run is included in this report.
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Affiliation(s)
- Andrew W. Liu
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, 904-0495, Japan
| | - Alejandro Villar-Briones
- Instrument Analysis Section, Okinawa Institute of Science and Technology, Onna-son, Okinawa, 904-0495, Japan
| | - Nicholas M. Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, 904-0495, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, 904-0495, Japan
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6
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The 2022 SLAS technology ten: Translating life sciences innovation. SLAS Technol 2022; 27:1-3. [DOI: 10.1016/j.slast.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Itoh TD, Horinouchi T, Uchida H, Takahashi K, Ozaki H. Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints. SLAS Technol 2021; 26:650-659. [PMID: 34167357 PMCID: PMC8641030 DOI: 10.1177/24726303211021790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/15/2022]
Abstract
In automated laboratories consisting of multiple different types of instruments, scheduling algorithms are useful for determining the optimal allocations of instruments to minimize the time required to complete experimental procedures. However, previous studies on scheduling algorithms for laboratory automation have not emphasized the time constraints by mutual boundaries (TCMBs) among operations, which is important in procedures involving live cells or unstable biomolecules. Here, we define the "scheduling for laboratory automation in biology" (S-LAB) problem as a scheduling problem for automated laboratories in which operations with TCMBs are performed by multiple different instruments. We formulate an S-LAB problem as a mixed-integer programming (MIP) problem and propose a scheduling method using the branch-and-bound algorithm. Simulations show that our method can find the optimal schedules of S-LAB problems that minimize overall execution time while satisfying the TCMBs. Furthermore, we propose the use of our scheduling method for the simulation-based design of job definitions and laboratory configurations.
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Affiliation(s)
- Takeshi D. Itoh
- Mathematical Informatics Laboratory, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Anchorage Works, Inc., Kobe, Hyogo, Japan
| | - Takaaki Horinouchi
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Laboratory for Multiscale Biosystem Dynamics, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | | | - Koichi Takahashi
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Matsuda T. Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing. PeerJ 2021; 9:e11875. [PMID: 34527435 PMCID: PMC8401820 DOI: 10.7717/peerj.11875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/06/2021] [Indexed: 11/20/2022] Open
Abstract
Large volumes of high-throughput sequencing data have been submitted to the Sequencing Read Archive (SRA). The lack of experimental metadata associated with the data makes reuse and understanding data quality very difficult. In the case of RNA sequencing (RNA-Seq), which reveals the presence and quantity of RNA in a biological sample at any moment, it is necessary to consider that gene expression responds over a short time interval (several seconds to a few minutes) in many organisms. Therefore, to isolate RNA that accurately reflects the transcriptome at the point of harvest, raw biological samples should be processed by freezing in liquid nitrogen, immersing in RNA stabilization reagent or lysing and homogenizing in RNA lysis buffer containing guanidine thiocyanate as soon as possible. As the number of samples handled simultaneously increases, the time until the RNA is protected can increase. Here, to evaluate the effect of different lag times in RNA protection on RNA-Seq data, we harvested CHO-S cells after 3, 5, 6, and 7 days of cultivation, added RNA lysis buffer in a time course of 15, 30, 45, and 60 min after harvest, and conducted RNA-Seq. These RNA samples showed high RNA integrity number (RIN) values indicating non-degraded RNA, and sequence data from libraries prepared with these RNA samples was of high quality according to FastQC. We observed that, at the same cultivation day, global trends of gene expression were similar across the time course of addition of RNA lysis buffer; however, the expression of some genes was significantly different between the time-course samples of the same cultivation day; most of these differentially expressed genes were related to apoptosis. We conclude that the time lag between sample harvest and RNA protection influences gene expression of specific genes. It is, therefore, necessary to know not only RIN values of RNA and the quality of the sequence data but also how the experiment was performed when acquiring RNA-Seq data from the database.
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