ShuttleTracker - Revision history

Redaktor at 18:24, 7 November 2023

2023-11-07T18:24:37Z

← Older revision		Revision as of 20:24, 7 November 2023
Line 55:		Line 55:
	* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->		* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->
	===Applications===		===Applications===
	* <span class="pmbm">Korwek Z</span>, <i>et al</i>. '''~~Non-self~~ RNA rewires IFNβ signaling: A mathematical model of the innate immune response''', ''Science Signaling'' (accepted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Korwek Z</span>, <i>et al</i>. '''Nonself RNA rewires IFNβ signaling: A mathematical model of the innate immune response''', ''Science Signaling'' (accepted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Grabowski F</span>, <i>et al</i>. '''Antagonism between viral infection and innate immunity at the single-cell level''', ''PLOS Pathogens'' <u>19</u>:e1011597 (2023) [https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed] [https://doi.org/10.1371/journal.ppat.1011597 CrossRef]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Grabowski F</span>, <i>et al</i>. '''Antagonism between viral infection and innate immunity at the single-cell level''', ''PLOS Pathogens'' <u>19</u>:e1011597 (2023) [https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed] [https://doi.org/10.1371/journal.ppat.1011597 CrossRef]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">		* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">

Redaktor at 18:24, 7 November 2023

2023-11-07T18:24:04Z

← Older revision		Revision as of 20:24, 7 November 2023
Line 55:		Line 55:
	* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->		* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->
	===Applications===		===Applications===
	* <span class="pmbm">~~Grabowski~~ F</span>, <i>et al</i>. '''~~Antagonism between viral infection and~~ innate ~~immunity at the single-cell level~~''' (~~submitted~~) [https://doi.org/10.1101/2022.11.18.~~517110~~ bioRxiv]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Korwek Z</span>, <i>et al</i>. '''Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response''', ''Science Signaling'' (accepted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">~~Korwek~~ Z</span>, <i>et al</i>. '''~~Non~~-~~self RNA rewires IFNβ signaling: A mathematical model of the innate immune response~~''' (~~submitted~~) [https://doi.org/10.~~1101~~/~~2022.01~~.30.~~478391 bioRxiv~~]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Grabowski F</span>, <i>et al</i>. '''Antagonism between viral infection and innate immunity at the single-cell level''', ''PLOS Pathogens'' <u>19</u>:e1011597 (2023) [https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed] [https://doi.org/10.1371/journal.ppat.1011597 CrossRef]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">		* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">

Redaktor at 08:41, 13 February 2023

2023-02-13T08:41:50Z

← Older revision		Revision as of 10:41, 13 February 2023
Line 17:		Line 17:

	===Stand-alone binary executables for Windows and Mac===		===Stand-alone binary executables for Windows and Mac===
	* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.3-x86_win64-setup.exe is '''~~dcd4fb642b68d1afca449ba5780035b2~~'''.<br/></accordion></div>		* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.3-x86_win64-setup.exe is '''d6a87dec0b6167ae12833821d6d8a208'''.<br/></accordion></div>

	* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>		* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>

Redaktor at 16:33, 2 February 2023

2023-02-02T16:33:41Z

← Older revision		Revision as of 18:33, 2 February 2023
Line 6:		Line 6:
	<div align="left" style="width:520px">		<div align="left" style="width:520px">
	S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> can detect stained cell nuclei, generate corresponding annular perinuclear extensions, quantify geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking.  Parameters of the image processing algorithms can be changed manually and the effects of these changes can be seen nearly immediately overlaid on currently displayed microscopic images.  A key capability of ShuttleTracker is that nuclear contours and tracks can be generated automatically and then corrected manually. The tool is scriptable. <br/><br/>		S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> can detect stained cell nuclei, generate corresponding annular perinuclear extensions, quantify geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking.  Parameters of the image processing algorithms can be changed manually and the effects of these changes can be seen nearly immediately overlaid on currently displayed microscopic images.  A key capability of ShuttleTracker is that nuclear contours and tracks can be generated automatically and then corrected manually. The tool is scriptable. <br/><br/>
	The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.5.3''' (~~January~~ 2023).		The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.5.3''' (February 2023).
	</div></div>		</div></div>
	<br/><br/>		<br/><br/>
Line 17:		Line 17:

	===Stand-alone binary executables for Windows and Mac===		===Stand-alone binary executables for Windows and Mac===
	* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.3-x86_win64-setup.exe is '''~~b8a8729c0b60688308dd51424df18ada~~'''.<br/></accordion></div>		* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.3-x86_win64-setup.exe is '''dcd4fb642b68d1afca449ba5780035b2'''.<br/></accordion></div>

	* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>		* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>

Redaktor at 10:06, 31 January 2023

2023-01-31T10:06:37Z

← Older revision		Revision as of 12:06, 31 January 2023
Line 17:		Line 17:

	===Stand-alone binary executables for Windows and Mac===		===Stand-alone binary executables for Windows and Mac===
	* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.1-x86_win64-setup.exe is '''~~b0792c78dc3d93d8007f9fac3508ce5b~~'''.<br/></accordion></div>		* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.3-x86_win64-setup.exe is '''b8a8729c0b60688308dd51424df18ada'''.<br/></accordion></div>

	* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>		* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>
Line 23:		Line 23:

	===Containers for Linux===		===Containers for Linux===
	* Docker container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1.Dockerfile shuttletracker-1.5.1.Dockerfile]<div class="accordion" id="accordion-docker"><accordion parent="accordion-docker" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		* Docker container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3.Dockerfile shuttletracker-1.5.3.Dockerfile]<div class="accordion" id="accordion-docker"><accordion parent="accordion-docker" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	docker build . -f shuttletracker-1.5.1.Dockerfile --tag st-container		docker build . -f shuttletracker-1.5.3.Dockerfile --tag st-container
	</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	docker run -e DISPLAY --net=host st-container		docker run -e DISPLAY --net=host st-container

Redaktor at 10:05, 31 January 2023

2023-01-31T10:05:47Z

← Older revision		Revision as of 12:05, 31 January 2023
Line 6:		Line 6:
	<div align="left" style="width:520px">		<div align="left" style="width:520px">
	S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> can detect stained cell nuclei, generate corresponding annular perinuclear extensions, quantify geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking.  Parameters of the image processing algorithms can be changed manually and the effects of these changes can be seen nearly immediately overlaid on currently displayed microscopic images.  A key capability of ShuttleTracker is that nuclear contours and tracks can be generated automatically and then corrected manually. The tool is scriptable. <br/><br/>		S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> can detect stained cell nuclei, generate corresponding annular perinuclear extensions, quantify geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking.  Parameters of the image processing algorithms can be changed manually and the effects of these changes can be seen nearly immediately overlaid on currently displayed microscopic images.  A key capability of ShuttleTracker is that nuclear contours and tracks can be generated automatically and then corrected manually. The tool is scriptable. <br/><br/>
	The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.5.1''' (~~September 2021~~).		The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.5.3''' (January 2023).
	</div></div>		</div></div>
	<br/><br/>		<br/><br/>
Line 12:		Line 12:

	===Documentation===		===Documentation===
	* User's manual:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-manual.pdf shuttletracker-1.5.1-manual.pdf]<br style="line-height: 100%; margin-bottom:14px">		* User's manual:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-manual.pdf shuttletracker-1.5.3-manual.pdf]<br style="line-height: 100%; margin-bottom:14px">
	* Tutorial and overview:  [{{SERVER}}/software/shuttletracker/release/previous/shuttletracker-1.3.0-tutorial.pdf shuttletracker-1.3.0-tutorial.pdf]<!--<span style="background:yellow"> ''' TODO ''' </span>--><br style="line-height: 100%; margin-bottom:6px">+ example input images:  [{{SERVER}}/software/shuttletracker/tutorial/March26_WellB_Pos09.zip March26_WellB_Pos09.zip] (~1.3 GB)<br style="line-height: 100%; margin-bottom:6px">+ example output from tracking analysis:  [{{SERVER}}/software/shuttletracker/tutorial/March26_WellB_Pos09.html March26_WellB_Pos09.html]		* Tutorial and overview:  [{{SERVER}}/software/shuttletracker/release/previous/shuttletracker-1.3.0-tutorial.pdf shuttletracker-1.3.0-tutorial.pdf]<!--<span style="background:yellow"> ''' TODO ''' </span>--><br style="line-height: 100%; margin-bottom:6px">+ example input images:  [{{SERVER}}/software/shuttletracker/tutorial/March26_WellB_Pos09.zip March26_WellB_Pos09.zip] (~1.3 GB)<br style="line-height: 100%; margin-bottom:6px">+ example output from tracking analysis:  [{{SERVER}}/software/shuttletracker/tutorial/March26_WellB_Pos09.html March26_WellB_Pos09.html]
	<br/>		<br/>

	===Stand-alone binary executables for Windows and Mac===		===Stand-alone binary executables for Windows and Mac===
	* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-x86_win64-setup.exe shuttletracker-1.5.1-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.1-x86_win64-setup.exe is '''b0792c78dc3d93d8007f9fac3508ce5b'''.<br/></accordion></div>		* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.1-x86_win64-setup.exe is '''b0792c78dc3d93d8007f9fac3508ce5b'''.<br/></accordion></div>

	* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>		* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>
Line 30:		Line 30:
	xhost +local:docker		xhost +local:docker
	</span></div></accordion></div>		</span></div></accordion></div>
	* Singularity container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1.recipe shuttletracker-1.5.1.recipe]<div class="accordion" id="accordion-singularity"><accordion parent="accordion-singularity" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		* Singularity container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3.recipe shuttletracker-1.5.3.recipe]<div class="accordion" id="accordion-singularity"><accordion parent="accordion-singularity" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	sudo singularity build --sandbox st shuttletracker-1.5.1.recipe		sudo singularity build --sandbox st shuttletracker-1.5.3.recipe
	</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	singularity exec --writable st /opt/local/bin/ShuttleTracker		singularity exec --writable st /opt/local/bin/ShuttleTracker
Line 38:		Line 38:
	===Source code===		===Source code===
	S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> source code is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/>		S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> source code is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/>
	* C++ source code:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-source.tar.gz shuttletracker-1.5.1-source.tar.gz]		* C++ source code:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-source.tar.gz shuttletracker-1.5.3-source.tar.gz]
	<div class="accordion" id="accordion-sourcecode"><accordion parent="accordion-sourcecode" heading="How to compile">Compilation on Linux, macOS, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way:		<div class="accordion" id="accordion-sourcecode"><accordion parent="accordion-sourcecode" heading="How to compile">Compilation on Linux, macOS, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way:
	<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	tar xfz shuttletracker-1.5.1-source.tar.gz		tar xfz shuttletracker-1.5.3-source.tar.gz
	cd shuttletracker-1.5.1-source		cd shuttletracker-1.5.3-source
	mkdir build && cd build		mkdir build && cd build
	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/		cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/

Redaktor at 14:54, 26 January 2023

2023-01-26T14:54:37Z

← Older revision		Revision as of 16:54, 26 January 2023
Line 17:		Line 17:

	===Stand-alone binary executables for Windows and Mac===		===Stand-alone binary executables for Windows and Mac===
	* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-x86_win64-setup.exe shuttletracker-1.5.1-x86_win64-setup.exe]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.1-x86_win64-setup.exe is '''b0792c78dc3d93d8007f9fac3508ce5b'''.<br/></accordion>		* Windows 64-bit installer:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-x86_win64-setup.exe shuttletracker-1.5.1-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="How to verify and run">COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.5.1-x86_win64-setup.exe is '''b0792c78dc3d93d8007f9fac3508ce5b'''.<br/></accordion></div>

	* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion>		* macOS application bundle (zipped "app", outdated):  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div>
	<br/>		<br/>

	===Containers for Linux===		===Containers for Linux===
	* Docker container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1.Dockerfile shuttletracker-1.5.1.Dockerfile]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		* Docker container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1.Dockerfile shuttletracker-1.5.1.Dockerfile]<div class="accordion" id="accordion-docker"><accordion parent="accordion-docker" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	docker build . -f shuttletracker-1.5.1.Dockerfile --tag st-container		docker build . -f shuttletracker-1.5.1.Dockerfile --tag st-container
	</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
Line 29:		Line 29:
	</span></div><br/>You will likely want to specify a filesystem location with images using docker run's flag <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">-v</span>. If the app fails to connect to the windows server, you may need to grant permission as follows: <div align="left"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		</span></div><br/>You will likely want to specify a filesystem location with images using docker run's flag <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">-v</span>. If the app fails to connect to the windows server, you may need to grant permission as follows: <div align="left"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	xhost +local:docker		xhost +local:docker
	</span></div></accordion>		</span></div></accordion></div>
	* Singularity container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1.recipe shuttletracker-1.5.1.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		* Singularity container:  [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1.recipe shuttletracker-1.5.1.recipe]<div class="accordion" id="accordion-singularity"><accordion parent="accordion-singularity" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	sudo singularity build --sandbox st shuttletracker-1.5.1.recipe		sudo singularity build --sandbox st shuttletracker-1.5.1.recipe
	</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	singularity exec --writable st /opt/local/bin/ShuttleTracker		singularity exec --writable st /opt/local/bin/ShuttleTracker
	</span></div></accordion><br/>		</span></div></accordion><div><br/>

	===Source code===		===Source code===
	S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> source code is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/>		S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> source code is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/>
	* C++ source code:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-source.tar.gz shuttletracker-1.5.1-source.tar.gz]		* C++ source code:   [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.1-source.tar.gz shuttletracker-1.5.1-source.tar.gz]
	<accordion parent="accordion" heading="How to compile">Compilation on Linux, macOS, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way:		<div class="accordion" id="accordion-sourcecode"><accordion parent="accordion-sourcecode" heading="How to compile">Compilation on Linux, macOS, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way:
	<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">		<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
	tar xfz shuttletracker-1.5.1-source.tar.gz		tar xfz shuttletracker-1.5.1-source.tar.gz
Line 47:		Line 47:
	make -j4 && make install		make -j4 && make install
	</span></div>		</span></div>
	More detailed instructions are provided in file COMPILING.md in the source code package. You may also have a look at how the build process is automated in a Singularity container recipe distributed in the source code distribution subdirectory distrib/singularity.<br/></accordion>		More detailed instructions are provided in file COMPILING.md in the source code package. You may also have a look at how the build process is automated in a Singularity container recipe distributed in the source code distribution subdirectory distrib/singularity.<br/></accordion></div>
	<br/>		<br/>

Redaktor at 17:35, 6 December 2022

2022-12-06T17:35:18Z

← Older revision		Revision as of 19:35, 6 December 2022
Line 54:		Line 54:
	====Primary citation====		====Primary citation====
	* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->		* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->
	===~~Published applications~~===		===Applications===
	* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''~~J Virol~~'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Grabowski F</span>, <i>et al</i>. '''Antagonism between viral infection and innate immunity at the single-cell level''' (submitted) [https://doi.org/10.1101/2022.11.18.517110 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
			* <span class="pmbm">Korwek Z</span>, <i>et al</i>. '''Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response''' (submitted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
			* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef]		* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef]

Redaktor at 16:31, 28 November 2022

2022-11-28T16:31:31Z

← Older revision		Revision as of 18:31, 28 November 2022
Line 55:		Line 55:
	* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->		* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->
	===Published applications===		===Published applications===
	* <span class="author">Czerkies M</span>, <i>et al</i>. '''~~RSV~~ protects bystander cells against ~~IAV~~ infection by triggering secretion of type I and type III interferons''', ''J Virol'' (~~accepted~~) [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">		* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''J Virol'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef]		* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef]

Redaktor at 09:49, 12 October 2022

2022-10-12T09:49:51Z

← Older revision		Revision as of 11:49, 12 October 2022
Line 55:		Line 55:
	* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->		* <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">-->
	===Published applications===		===Published applications===
			* <span class="author">Czerkies M</span>, <i>et al</i>. '''RSV protects bystander cells against IAV infection by triggering secretion of type I and type III interferons''', ''J Virol'' (accepted) [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">		* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px">
	* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef]		* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef]