Journal:Ten simple rules for managing laboratory information - Revision history

Shawndouglas: /* Capture context in notebook entries */ Fix

2024-04-11T18:59:35Z

Capture context in notebook entries: Fix

← Older revision		Revision as of 18:59, 11 April 2024
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	===Capture context in notebook entries===		===Capture context in notebook entries===
	Organizing data in databases and capturing essential metadata describing the data production process can greatly simplify the process of documenting research projects in [[laboratory notebook]]s.<ref name=":19">{{Cite journal \|last=Nussbeck \|first=Sara Y \|last2=Weil \|first2=Philipp \|last3=Menzel \|first3=Julia \|last4=Marzec \|first4=Bartlomiej \|last5=Lorberg \|first5=Kai \|last6=Schwappach \|first6=Blanche \|date=2014-06 \|title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity \|url=https://www.embopress.org/doi/10.15252/embr.201338358 \|journal=EMBO reports \|language=en \|volume=15 \|issue=6 \|pages=631–634 \|doi=10.15252/embr.201338358 \|issn=1469-221X \|pmc=PMC4197872 \|pmid=24833749}}</ref> Instead of needing to include copies of the protocols and the raw data produced by the experiment, the notebook entry can focus on the context, purpose, and results of the experiment. In the case of ELNs (e.g., [[~~SciNote~~, LLC\|SciNote]], [[Vendor:LabArchives, LLC\|LabArchives]], and [[Vendor:Bio-ITech BV\|eLabJournal]]), entries can benefit from providing links to previous notebook entries, the experimental and analytical protocols used, and the datasets produced by the workflows. ELNs also bring additional benefits like portability, standardized templates, and improved sharing, and improved reproducibility. Finally, notebook entries should include the interpretation of the data as well as a conclusion pointing to the next experiment. The presence of this rich metadata and detailed provenance is critical to ensuring the FAIR principles are being met and your experiments are reproducible.<ref name=":12" />		Organizing data in databases and capturing essential metadata describing the data production process can greatly simplify the process of documenting research projects in [[laboratory notebook]]s.<ref name=":19">{{Cite journal \|last=Nussbeck \|first=Sara Y \|last2=Weil \|first2=Philipp \|last3=Menzel \|first3=Julia \|last4=Marzec \|first4=Bartlomiej \|last5=Lorberg \|first5=Kai \|last6=Schwappach \|first6=Blanche \|date=2014-06 \|title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity \|url=https://www.embopress.org/doi/10.15252/embr.201338358 \|journal=EMBO reports \|language=en \|volume=15 \|issue=6 \|pages=631–634 \|doi=10.15252/embr.201338358 \|issn=1469-221X \|pmc=PMC4197872 \|pmid=24833749}}</ref> Instead of needing to include copies of the protocols and the raw data produced by the experiment, the notebook entry can focus on the context, purpose, and results of the experiment. In the case of ELNs (e.g., [[Vendor:sciNote, LLC\|SciNote]], [[Vendor:LabArchives, LLC\|LabArchives]], and [[Vendor:Bio-ITech BV\|eLabJournal]]), entries can benefit from providing links to previous notebook entries, the experimental and analytical protocols used, and the datasets produced by the workflows. ELNs also bring additional benefits like portability, standardized templates, and improved sharing, and improved reproducibility. Finally, notebook entries should include the interpretation of the data as well as a conclusion pointing to the next experiment. The presence of this rich metadata and detailed provenance is critical to ensuring the FAIR principles are being met and your experiments are reproducible.<ref name=":12" />

	==Rule 7: Separate parameters and variables==		==Rule 7: Separate parameters and variables==

Shawndouglas: Text replacement - "\[\[Benchling, Inc.(.*)" to "[[Vendor:Benchling, Inc.$1"

2024-04-04T22:34:48Z

Text replacement - "\[\[Benchling, Inc.(.*)" to "[[Vendor:Benchling, Inc.$1"

← Older revision		Revision as of 22:34, 4 April 2024
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	All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>		All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>

	Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[Vendor:LabVantage Solutions, Inc.\|LabVantage]], and [[Vendor:TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.		Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Vendor:Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[Vendor:LabVantage Solutions, Inc.\|LabVantage]], and [[Vendor:TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.

	Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.		Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.

Shawndouglas: Text replacement - "\[\[LabArchives, LLC(.*)" to "[[Vendor:LabArchives, LLC$1"

2024-04-03T20:36:36Z

Text replacement - "\[\[LabArchives, LLC(.*)" to "[[Vendor:LabArchives, LLC$1"

← Older revision		Revision as of 20:36, 3 April 2024
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	===Capture context in notebook entries===		===Capture context in notebook entries===
	Organizing data in databases and capturing essential metadata describing the data production process can greatly simplify the process of documenting research projects in [[laboratory notebook]]s.<ref name=":19">{{Cite journal \|last=Nussbeck \|first=Sara Y \|last2=Weil \|first2=Philipp \|last3=Menzel \|first3=Julia \|last4=Marzec \|first4=Bartlomiej \|last5=Lorberg \|first5=Kai \|last6=Schwappach \|first6=Blanche \|date=2014-06 \|title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity \|url=https://www.embopress.org/doi/10.15252/embr.201338358 \|journal=EMBO reports \|language=en \|volume=15 \|issue=6 \|pages=631–634 \|doi=10.15252/embr.201338358 \|issn=1469-221X \|pmc=PMC4197872 \|pmid=24833749}}</ref> Instead of needing to include copies of the protocols and the raw data produced by the experiment, the notebook entry can focus on the context, purpose, and results of the experiment. In the case of ELNs (e.g., [[SciNote, LLC\|SciNote]], [[LabArchives, LLC\|LabArchives]], and [[Vendor:Bio-ITech BV\|eLabJournal]]), entries can benefit from providing links to previous notebook entries, the experimental and analytical protocols used, and the datasets produced by the workflows. ELNs also bring additional benefits like portability, standardized templates, and improved sharing, and improved reproducibility. Finally, notebook entries should include the interpretation of the data as well as a conclusion pointing to the next experiment. The presence of this rich metadata and detailed provenance is critical to ensuring the FAIR principles are being met and your experiments are reproducible.<ref name=":12" />		Organizing data in databases and capturing essential metadata describing the data production process can greatly simplify the process of documenting research projects in [[laboratory notebook]]s.<ref name=":19">{{Cite journal \|last=Nussbeck \|first=Sara Y \|last2=Weil \|first2=Philipp \|last3=Menzel \|first3=Julia \|last4=Marzec \|first4=Bartlomiej \|last5=Lorberg \|first5=Kai \|last6=Schwappach \|first6=Blanche \|date=2014-06 \|title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity \|url=https://www.embopress.org/doi/10.15252/embr.201338358 \|journal=EMBO reports \|language=en \|volume=15 \|issue=6 \|pages=631–634 \|doi=10.15252/embr.201338358 \|issn=1469-221X \|pmc=PMC4197872 \|pmid=24833749}}</ref> Instead of needing to include copies of the protocols and the raw data produced by the experiment, the notebook entry can focus on the context, purpose, and results of the experiment. In the case of ELNs (e.g., [[SciNote, LLC\|SciNote]], [[Vendor:LabArchives, LLC\|LabArchives]], and [[Vendor:Bio-ITech BV\|eLabJournal]]), entries can benefit from providing links to previous notebook entries, the experimental and analytical protocols used, and the datasets produced by the workflows. ELNs also bring additional benefits like portability, standardized templates, and improved sharing, and improved reproducibility. Finally, notebook entries should include the interpretation of the data as well as a conclusion pointing to the next experiment. The presence of this rich metadata and detailed provenance is critical to ensuring the FAIR principles are being met and your experiments are reproducible.<ref name=":12" />

	==Rule 7: Separate parameters and variables==		==Rule 7: Separate parameters and variables==

Shawndouglas: Text replacement - "\[\[TeselaGen Biotechnology, Inc.(.*)" to "[[Vendor:TeselaGen Biotechnology, Inc.$1"

2024-03-29T17:21:34Z

Text replacement - "\[\[TeselaGen Biotechnology, Inc.(.*)" to "[[Vendor:TeselaGen Biotechnology, Inc.$1"

← Older revision		Revision as of 17:21, 29 March 2024
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	All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>		All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>

	Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[Vendor:LabVantage Solutions, Inc.\|LabVantage]], and [[TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.		Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[Vendor:LabVantage Solutions, Inc.\|LabVantage]], and [[Vendor:TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.

	Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.		Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.

Shawndouglas: Text replacement - "\[\[Bio-ITech BV(.*)" to "[[Vendor:Bio-ITech BV$1"

2024-03-29T16:19:35Z

Text replacement - "\[\[Bio-ITech BV(.*)" to "[[Vendor:Bio-ITech BV$1"

← Older revision		Revision as of 16:19, 29 March 2024
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	===Capture context in notebook entries===		===Capture context in notebook entries===
	Organizing data in databases and capturing essential metadata describing the data production process can greatly simplify the process of documenting research projects in [[laboratory notebook]]s.<ref name=":19">{{Cite journal \|last=Nussbeck \|first=Sara Y \|last2=Weil \|first2=Philipp \|last3=Menzel \|first3=Julia \|last4=Marzec \|first4=Bartlomiej \|last5=Lorberg \|first5=Kai \|last6=Schwappach \|first6=Blanche \|date=2014-06 \|title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity \|url=https://www.embopress.org/doi/10.15252/embr.201338358 \|journal=EMBO reports \|language=en \|volume=15 \|issue=6 \|pages=631–634 \|doi=10.15252/embr.201338358 \|issn=1469-221X \|pmc=PMC4197872 \|pmid=24833749}}</ref> Instead of needing to include copies of the protocols and the raw data produced by the experiment, the notebook entry can focus on the context, purpose, and results of the experiment. In the case of ELNs (e.g., [[SciNote, LLC\|SciNote]], [[LabArchives, LLC\|LabArchives]], and [[Bio-ITech BV\|eLabJournal]]), entries can benefit from providing links to previous notebook entries, the experimental and analytical protocols used, and the datasets produced by the workflows. ELNs also bring additional benefits like portability, standardized templates, and improved sharing, and improved reproducibility. Finally, notebook entries should include the interpretation of the data as well as a conclusion pointing to the next experiment. The presence of this rich metadata and detailed provenance is critical to ensuring the FAIR principles are being met and your experiments are reproducible.<ref name=":12" />		Organizing data in databases and capturing essential metadata describing the data production process can greatly simplify the process of documenting research projects in [[laboratory notebook]]s.<ref name=":19">{{Cite journal \|last=Nussbeck \|first=Sara Y \|last2=Weil \|first2=Philipp \|last3=Menzel \|first3=Julia \|last4=Marzec \|first4=Bartlomiej \|last5=Lorberg \|first5=Kai \|last6=Schwappach \|first6=Blanche \|date=2014-06 \|title=The laboratory notebook in the 21 st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity \|url=https://www.embopress.org/doi/10.15252/embr.201338358 \|journal=EMBO reports \|language=en \|volume=15 \|issue=6 \|pages=631–634 \|doi=10.15252/embr.201338358 \|issn=1469-221X \|pmc=PMC4197872 \|pmid=24833749}}</ref> Instead of needing to include copies of the protocols and the raw data produced by the experiment, the notebook entry can focus on the context, purpose, and results of the experiment. In the case of ELNs (e.g., [[SciNote, LLC\|SciNote]], [[LabArchives, LLC\|LabArchives]], and [[Vendor:Bio-ITech BV\|eLabJournal]]), entries can benefit from providing links to previous notebook entries, the experimental and analytical protocols used, and the datasets produced by the workflows. ELNs also bring additional benefits like portability, standardized templates, and improved sharing, and improved reproducibility. Finally, notebook entries should include the interpretation of the data as well as a conclusion pointing to the next experiment. The presence of this rich metadata and detailed provenance is critical to ensuring the FAIR principles are being met and your experiments are reproducible.<ref name=":12" />

	==Rule 7: Separate parameters and variables==		==Rule 7: Separate parameters and variables==

Shawndouglas: Text replacement - "\[\[LabVantage Solutions, Inc.(.*)" to "[[Vendor:LabVantage Solutions, Inc.$1"

2024-03-28T01:26:15Z

Text replacement - "\[\[LabVantage Solutions, Inc.(.*)" to "[[Vendor:LabVantage Solutions, Inc.$1"

← Older revision		Revision as of 01:26, 28 March 2024
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	All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>		All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>

	Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[LabVantage Solutions, Inc.\|LabVantage]], and [[TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.		Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[Vendor:LabVantage Solutions, Inc.\|LabVantage]], and [[TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.

	Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.		Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.

Shawndouglas: Text replacement - "LabWare" to "LabWare"

2024-03-28T00:32:59Z

Text replacement - "LabWare" to "LabWare"

← Older revision		Revision as of 00:32, 28 March 2024
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	All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>		All the data produced by your lab are derived from things you have purchased, including supplies (consumables), equipment, and contract manufactured reagents, such as oligonucleotides or synthetic genes. In many cases, data (and [[metadata]]) on items in your inventory may be just as important as experimentally derived data, and as such, should be managed according to the [[Journal:The FAIR Guiding Principles for scientific data management and stewardship\|FAIR (findable, accessible, interoperable, and reusable) principles]].<ref name=":12">{{Cite journal \|last=Wilkinson \|first=Mark D. \|last2=Dumontier \|first2=Michel \|last3=Aalbersberg \|first3=IJsbrand Jan \|last4=Appleton \|first4=Gabrielle \|last5=Axton \|first5=Myles \|last6=Baak \|first6=Arie \|last7=Blomberg \|first7=Niklas \|last8=Boiten \|first8=Jan-Willem \|last9=da Silva Santos \|first9=Luiz Bonino \|last10=Bourne \|first10=Philip E. \|last11=Bouwman \|first11=Jildau \|date=2016-03-15 \|title=The FAIR Guiding Principles for scientific data management and stewardship \|url=https://www.nature.com/articles/sdata201618 \|journal=Scientific Data \|language=en \|volume=3 \|issue=1 \|pages=160018 \|doi=10.1038/sdata.2016.18 \|issn=2052-4463 \|pmc=PMC4792175 \|pmid=26978244}}</ref> Assembling an inventory of supplies and equipment with their associated locations can be handled in a few weeks by junior personnel without major interruption of laboratory operations, although establishing a thorough inventory may be more difficult and time-consuming for smaller labs with fewer members. Nevertheless, managing your lab inventory provides an immediate return on investment by positively impacting laboratory operations in several ways. People can quickly find the supplies and equipment they need to work, supplies are ordered with appropriate advance notice to minimize work stoppage, and data variation is reduced due to standardized supplies and the ability to track lot numbers easily (Fig. 1).<ref name=":6" /><ref name=":13">{{Cite journal \|last=Perkel \|first=Jeffrey M. \|date=2015-08-06 \|title=Lab-inventory management: Time to take stock \|url=https://www.nature.com/articles/524125a \|journal=Nature \|language=en \|volume=524 \|issue=7563 \|pages=125–126 \|doi=10.1038/524125a \|issn=0028-0836}}</ref><ref>{{Cite journal \|last=Foster \|first=Barbara L. \|date=2005-09-01 \|title=The Chemical Inventory Management System in academia \|url=https://pubs.acs.org/doi/10.1016/j.chs.2005.01.019 \|journal=Chemical Health & Safety \|language=en \|volume=12 \|issue=5 \|pages=21–25 \|doi=10.1016/j.chs.2005.01.019 \|issn=1074-9098}}</ref>

	Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[LabWare, Inc.\|LabWare]], [[LabVantage Solutions, Inc.\|LabVantage]], and [[TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.		Many labs still use Excel to keep track of inventory despite the existence of several more sophisticated databases and LIMS (e.g., [[Benchling, Inc.\|Benchling]], Quartzy, [[GenoFAB, Inc.\|GenoFAB]], [[Vendor:LabWare, Inc.\|LabWare]], [[LabVantage Solutions, Inc.\|LabVantage]], and [[TeselaGen Biotechnology, Inc.\|TeselaGen]]).<ref name=":13" /> These can facilitate real-time inventory tracking unlike a static document, increasing the findability and accessibility of inventory data. While some systems are specialized for certain types of inventories (e.g., animal colonies or frozen reagents), others are capable of tracking any type of reagent or item imaginable.<ref name=":13" /> When considering what items to keep track of, there are three main considerations: expiration, maintenance, and ease of access.

	Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.		Most labs manage their supplies through periodic cleanups of the lab, during which they sort through freezers, chemical cabinets, and other storage areas; review their contents; and dispose of supplies that are past their expiration date or are no longer useful. By actively tracking expiration dates and reagent use in a LIMS, you can decrease the frequency of such cleanups since the LIMS will alert users when expiration dates are approaching or when supplies are running low. This can prevent costly items from being wasted because they are expired or forgotten, and furthermore, the cost of products can be tracked and used to inform which experiments are performed.

Shawndouglas: Finished adding rest of content.

2024-03-19T16:30:04Z

Finished adding rest of content.

Show changes

Shawndouglas: Saving and adding more.

2024-03-19T14:45:57Z

Saving and adding more.

← Older revision		Revision as of 14:45, 19 March 2024
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	\|affiliations = Colorado State University, University of Groningen, University of Virginia, Boston University, Imperial College, University of Bristol, Lawrence Berkeley National Laboratory, US Department of Energy Agile BioFoundry, US Department of Energy Joint BioEnergy Institute, LanzaTech, University of Washington Medicine, Washington University in St. Louis, Cedars-Sinai Medical Centet, University of Colorado Boulder, University of California Irvine - Irvine		\|affiliations = Colorado State University, University of Groningen, University of Virginia, Boston University, Imperial College, University of Bristol, Lawrence Berkeley National Laboratory, US Department of Energy Agile BioFoundry, US Department of Energy Joint BioEnergy Institute, LanzaTech, University of Washington Medicine, Washington University in St. Louis, Cedars-Sinai Medical Centet, University of Colorado Boulder, University of California Irvine - Irvine
	\|contact = Email: jean dot peccoud at colostate dot edu		\|contact = Email: jean dot peccoud at colostate dot edu
	\|editors =		\|editors = Markel, Scott
	\|pub_year = 2023		\|pub_year = 2023
	\|vol_iss = '''19'''(12)		\|vol_iss = '''19'''(12)
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	Laboratory operations and the data they produce are increasingly dependent on operations that take place outside of the lab. For example, the results of a [[polymerase chain reaction]] (PCR) assay will be affected by the primer design algorithm and the values of its parameters. They will also be affected by the quality of the primers manufactured by a specialized service provider. Even though the primer design and primer synthesis are not taking place in the lab, they are an integral part of the process of generating PCR data. They should therefore be captured in data flows (see prior Rule 8). Furthermore, the software and computational steps used to design experiments and analyze data they produce must also be properly recorded, to identify as many factors that may affect the data produced in the lab as possible.		Laboratory operations and the data they produce are increasingly dependent on operations that take place outside of the lab. For example, the results of a [[polymerase chain reaction]] (PCR) assay will be affected by the primer design algorithm and the values of its parameters. They will also be affected by the quality of the primers manufactured by a specialized service provider. Even though the primer design and primer synthesis are not taking place in the lab, they are an integral part of the process of generating PCR data. They should therefore be captured in data flows (see prior Rule 8). Furthermore, the software and computational steps used to design experiments and analyze data they produce must also be properly recorded, to identify as many factors that may affect the data produced in the lab as possible.

			===Increase the accessibility of your work===
			There are several ways to place your lab in the greater scientific context and increase reproducibility. As discussed, using standardized, non-proprietary file types can increase ease of access within a lab and across groups. [14,51] You may also choose to make your data and source code public in an online repository to comply with journal requirements, increase transparency, or allow access to your data by other groups. [67] In addition, data exchange standards, such as the Synthetic Biology Open Language [68,69], increase the accessibility and reproducibility of your work.

			===Practice makes perfect===
			Whereas traditional data management methods can restrict your analyses to limited subsets of data, centralized information management systems (encompassing relational and NoSQL databases, metadata, sample tracking, etc.) facilitate the analysis of previously disparate datasets. Given the increasing availability and decreasing cost of information management systems, it is now possible for labs to produce, document, and track a seemingly endless amount of samples and data, and use these to inform their research directions in previously impossible ways. When establishing your LIMS, or incorporating new experiments, it is better to capture more data than less. As you standardize your workflows (see prior Rule 8), you should be able to establish clear metrics defining the success of an experiment and to scale the amount of the data you collect as needed.

			While there are plenty of existing ELN and LIMS options to choose from (see Rule 6 and Rule 2, respectively), none are a turnkey solution. All data management systems require configuration and optimization for an individual lab. Each option has its own benefits and limitations, which your group must weigh. Coupled with the need to store your data with multiple backup options, thoughtful management practices are necessary to make any of these technologies work for your lab. The 10 rules discussed here should provide both a starting place and continued resource in the development of your LIMS. Remember that developing a LIMS is not a one-time event; all lab members must contribute to the maintenance of the LIMS and document their supplies, samples, and experiments in a timely manner. Although it might be an overwhelming process to begin with, careful data management will quickly benefit the data, users, and lab through saved time, standardized practices, and more powerful insights. [17,18]

			==Conclusions==
			Imparting a strong organizational structure for your lab information can ultimately save you both time and money if properly maintained. We present these 10 rules to help you build a strong foundation in managing your lab information so that you may avoid the costly and frustrating mistakes we have made over the years. By implementing these 10 rules, you should see some immediate benefits of your newfound structure, perhaps in the form of extra fridge space or fewer delays waiting for a reagent you did not realize was exhausted. In time, you will gain deep insights into your workflows and more easily analyze and report your data. The goal of these rules is also to spur conversation about lab management systems both between and within labs as there is no one-size-fits-all solution for lab management. While these rules provide a great starting point, the topic of how to manage lab information is something that must be a constant dialogue. The lab needs to discuss what is working and what is not working to assess and adjust the system to meet the needs of the lab. This dialogue must also be extended to all new members of the lab as many of these organizational steps may not be intuitive. It is critical to train new members extensively and to ensure that they are integrated into the lab’s common culture or else you risk falling back into bad practices. If properly trained, lab members will propagate and benefit from the organizational structure of the lab.

			==Acknowledgements==
			===Funding===
			J.P., S.H., C.K., K.M., and C.-T.B. are supported by the National Science Foundation (award #2123367) and the National Institutes of Health (R01GM147816, T32GM132057). T.S.M. is supported by the Defense Advanced Research Projects Agency (N660012324032), the Office of Naval Research (N00014-21-1-2206), U.S. Environmental Protection Agency (84020501), the National Institutes of Health (R01 AT009741), and the National Science Foundation (MCB-2001743 and EF-2222403). C.J.M. is supported by the National Science Foundation (MCB-2231864) and the National Institutes Standards and Technology (70NANB21H103). D.A.N. is supported by the National Institutes of Health (R00HD098330 and DP2AI171121). B.M. and L.U.A. are supported by the National Institutes of Health (R35 GM124747). T.E.G. was supported by a Royal Society University Research Fellowship grant UF160357, a Turing Fellowship from The Alan Turing Institute under the EPSRC grant EP/N510129/1. W.Z. is supported by the National Institutes of Health (R01GM144961) and the National Science Foundation (IOS1922701).

			This work was part of the [https://agilebiofoundry.org/ Agile BioFoundry] supported by the U.S. Department of Energy, Energy Efficiency and Renewable Energy, Bioenergy Technologies Office, and was part of the DOE [https://www.jbei.org/ Joint BioEnergy Institute] supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy.

			The views and opinions of the authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility or the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed or represents that its use would not infringe privately owned rights. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the [https://www.energy.gov/doe-public-access-plan DOE Public Access Plan]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

			===Competing interests===
			I have read the journal’s policy, and the authors of this manuscript have the following competing interests: J.P., S.P., and K.M. have a financial interest in GenoFAB, Inc. M.K. is an employee of LanzaTech. N.J.H. has a financial interest in TeselaGen Biotechnology, Inc. and Ansa Biotechnologies, Inc. GenoFAB, Inc. and TeselaGen Biotechnology, Inc. provide research information management systems. These companies may benefit or be perceived as benefiting from this publication.

	==References==		==References==

Shawndouglas at 22:57, 18 March 2024

2024-03-18T22:57:14Z

← Older revision		Revision as of 22:57, 18 March 2024
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	\|website = [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011652 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011652]		\|website = [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011652 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011652]
	\|download = [https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011652&type=printable https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011652&type=printable] (PDF)		\|download = [https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011652&type=printable https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011652&type=printable] (PDF)
			}}
			{{ombox
			\| type = notice
			\| image = [[Image:Emblem-important-yellow.svg\|40px]]
			\| style = width: 500px;
			\| text = This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed.
	}}		}}
	==Abstract==		==Abstract==