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= The Archive =
= The Archive =


'The Archives' - Collection of animal tissues, digital media, document boxes, the details of which this page is concerned with.<Br>
'The Archives' - Collection of animal tissues, digital media, document boxes, the details of which this page is concerned with. Previously called NRA, now NURA. Consider using the Wiki's Search function if you have something specific you are looking for.<Br>


* [[Archive Terminology]]: A list of acronyms commonly used within the archives. Everything from institution names to projects to departments.
* [[Archive Terminology]]: A list of acronyms commonly used within the archives. Everything from institution names to projects to departments.
* [[Archive Technology]]: A list of Software (Databases, subsystems, etc. used within the historical NRA archive)
* [[Archive Boxes]]: Physical boxes of the archives. Their storage, categorization, contents, etc.
* [[Archive Tissues]]: Slides, Paraffin blocks, etc.
* [[Archive Methods]]
* [[Medical Records]]
* [[Archive Database]]


* [http://janus-cloud2.s3.amazonaws.com/www/dog_tissues/reports_broken/red_book.pdf Red Book]


= Software =
== People ==
[http://www.roelee.co.uk/RL_Intro.html RoeLee] - Software which is a Histopathology and Necropsy system. There are references to this system in the Optical Archives. It is unclear what data this software was specifically concerned with storing, much less whether we actually have the data or the corresponding software. However, since there are mentions of lab notebooks, if it were the case that lab notebooks were being stored in an electronic form, this would likely be of great interest.<br>
[https://jamanetwork.com/journals/jama/article-abstract/409188 Papyrus] - Software: A reference database / Bibliography program whose main function is to store and retrieve bibliographic references in any format. "This particular software is necessary for compatibility with collaborators in Europe and Japan." See <code>PAP.MEM</code> institutional context and <code>PAPR.DOC</code> for general documentation.<br>
 
 
= Technology: Backup Software and Physical Media =
Platter - Seemingly the name that was used to describe a single-side of the MO media. A platter-code would be the label of such a volume<Br>
[https://en.wikipedia.org/wiki/9_track_tape 9-track] - A type of reel-to-reel magnetic tape media. We have (so far) discovered two of these tapes, however, digitization efforts are deferred as they are likely already contained within the optical HRAD archive which has been made available on the NU Radonc disk store.<br>
Alphatronix - Possibly an old backup system or software. References to it in the MO archives are present. Examine EODDIR, EO.SYS, EOVERIFY.EXE<br>
XCOPY - An old DOS command often used to make backups / archives. Commonly used when it is necessary to work with entire directories.<br>
[https://en.wikipedia.org/wiki/Magneto-optical_drive MO] - Magneto Optical: A type of media which encased in plastic which on the inside looks like a compact disc. Rewriteable.<br>
[https://en.wikipedia.org/wiki/PC_Tools_(software) PCT] - Pc Tools. Old DOS software but relevant because compressed files exist which utilized Central Point Backup<br>
 
= People =
<code>PERSON.DB</code> and <code>PHONE.DB</code>May be of interest...<br>
<code>PERSON.DB</code> and <code>PHONE.DB</code>May be of interest...<br>
SKS - Sean K. Smith: Computer Scientist<br>
SKS - Sean K. Smith: Computer Scientist<br>
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Bill Morgan - <br>
Bill Morgan - <br>
Tom Fritz - <br>
Tom Fritz - <br>
James F. Park* - PI on [[Experiment 140]]<br>
Cliff Burton - Database Administrator at LEHR<br>
Charles Leonard Sanders (aka C.L. Sanders) (aka 'Chuck') - PNL/PNNL/Battelle Rodent Studies<br>
<p><nowiki>* Deceased.</nowiki></p>
<p><nowiki>* Deceased.</nowiki></p>


= Timeline of experiments and major archive events =
== Timeline of experiments and major archive events ==
* 1989 - Creation of the NRA
* 1989 - Creation of the NRA
* 1992 - ITRI files donated to the NRA. [https://ustur.wsu.edu/nra-document-archives/ UC Davis Collection donated to PNL.]
* 1994 - Transfer of Information to the National Radiobiology Archives: In 1994, the records stored on the VAX computer were transferred to the PC environment and converted to PARADOX tables. This was part of the process of donating the information to the National Radiobiology Archives
* 1994 - Morat.txt "DOE/RL announced today an indefinite moratorium on ADP equipment and furniture acquisition. This memo describes impacts of the moratorium on operation of the Health Risk Assessment Department (HRAD).
* 1994 - Morat.txt "DOE/RL announced today an indefinite moratorium on ADP equipment and furniture acquisition. This memo describes impacts of the moratorium on operation of the Health Risk Assessment Department (HRAD).
* 1996 - The NRA program was transferred from Pacific Northwest National Laboratory (PNNL), operating for the U.S. Department of Energy, to the USTUR operations at WSU in 1996. The initial transfer included a limited collection of paraffin-embedded tissue blocks, microscope slides, clinical notes, pathologist observations, and several pieces of computer equipment. These specimens have been cataloged and are housed with the USTUR archives. Although the original archive collection at the NRA included formalin and/or alcohol-fixed tissues and thousands of radiographic films, concerns over the storage of such hazardous materials, coupled with budgetary constraints, led to proper disposal of these items which therefore were not transferred to the Registries with the other materials.  
* 1996 - The NRA program was transferred from Pacific Northwest National Laboratory (PNNL), operating for the U.S. Department of Energy, to the USTUR operations at WSU in 1996. The initial transfer included a limited collection of paraffin-embedded tissue blocks, microscope slides, clinical notes, pathologist observations, and several pieces of computer equipment. These specimens have been cataloged and are housed with the USTUR archives. Although the original archive collection at the NRA included formalin and/or alcohol-fixed tissues and thousands of radiographic films, concerns over the storage of such hazardous materials, coupled with budgetary constraints, led to proper disposal of these items which therefore were not transferred to the Registries with the other materials.  
* 2006 - PNL Materials transferred to USTUR as WSU.
* 2010 - All materials associated with the NRA program were transferred to Northwestern University.
* 2010 - All materials associated with the NRA program were transferred to Northwestern University.
* 2010 - "Beaglecon" happened in Richland, Washington in July of 2010. At this gathering, many key figures were present (Tom Fritz, Chuck Watson, etc.). This is where Ben was given data from Chuck Watson: it has been placed onto a 2.5" USB "Iomega" External Hard drive. There are also audio recording of this event (presumably taken by Ben), which Tanja mentioned she would like to have transcribed via software or service.
* 2010 - "Beaglecon" happened in Richland, Washington in July of 2010. At this gathering, many key figures were present (Tom Fritz, Chuck Watson, etc.). This is where Ben was given data from Chuck Watson: it has been placed onto a 2.5" USB "Iomega" External Hard drive. There are also audio recording of this event (presumably taken by Ben), which Tanja mentioned she would like to have transcribed via software or service.
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* [https://janus-cloud2.s3.amazonaws.com/www/nira/images/5/5d/Beagle_Data_Congress_Day_2_4-5.mp3 Documentation Fun by Watson]
* [https://janus-cloud2.s3.amazonaws.com/www/nira/images/5/5d/Beagle_Data_Congress_Day_2_4-5.mp3 Documentation Fun by Watson]


= Boxes =
= Todo =
* Barcodes may have been generated by a software from "Worthington Data Solutions"
* Unearth EasyCASE software. Open mystery files. SKS seems mostly responsible for leading the charge in using this software...
* The Paper archives consist of bankers boxes located at Pickens-Kane in Chicago
* Maybe we want to have a chat with SKS?
** HRAD51\PNL9NRA\JNS makes mention of a physical box inventory
* Move vm to linux, automate .ps to .pdf print functionality.
** Things to search to try and find references to boxen:
* Controls Database
** NRA Barcodes:
* Figure out what the deal is with Focus Hierarchical Database.
*** 005096 or P005096
*** D000278


= Unknown Terminology =
= Unknown Terminology =
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RIB - Possibly Diagnosis codes similar to SNODOG???????? Possibly "Radioanalysis Inventory for Biology System Description"<br>
RIB - Possibly Diagnosis codes similar to SNODOG???????? Possibly "Radioanalysis Inventory for Biology System Description"<br>
PAL - Some manner of computer scripts. Also Object PAL.<br>
PAL - Some manner of computer scripts. Also Object PAL.<br>
Datatrieve - Some mischief having to do with VAX maybe????<br>
IRDS - Information Resource Dictionary System. A horrible little acronym that says nothing about what it actually is.<br>
IRDS - Information Resource Dictionary System. A horrible little acronym that says nothing about what it actually is.<br>
RDM - NOT CLEAR. There is a reference in <code>960102/HISTO/README.TXT</code>: "These files are intended for use by the RDM consultant." Any chance this could be related to Roelee? <code>PNL_DOC.SAM</code> also references "Walt developed a report procedure, named NRA, on his RDM database management system." <code>NRA_U_CM.DTR</code> suggests this is related to a Microvax in Utah "The input file is a report generated by RDM on the Utah micro VAX."
[[RDM]] - NOT CLEAR. There is a reference in <code>960102/HISTO/README.TXT</code>: "These files are intended for use by the RDM consultant." Any chance this could be related to Roelee? <code>PNL_DOC.SAM</code> also references "Walt developed a report procedure, named NRA, on his RDM database management system." <code>NRA_U_CM.DTR</code> suggests this is related to a Microvax in Utah "The input file is a report generated by RDM on the Utah micro VAX."
 
= Tissues =
 
== Paraffin Block Codes ==
* LD1-7 = 7 standard samples for the left diaphragmatic  lobe of the lung
* RA1-5 = 5 standard samples for the right apical  lobe of the lung
* RC1-5 = 5 standard samples for the right cardiac  lobe of the lung


= Queued questions for persons of interest =
= Queued questions for persons of interest =

Latest revision as of 20:22, 20 October 2023

The Archive

'The Archives' - Collection of animal tissues, digital media, document boxes, the details of which this page is concerned with. Previously called NRA, now NURA. Consider using the Wiki's Search function if you have something specific you are looking for.

People

PERSON.DB and PHONE.DBMay be of interest...
SKS - Sean K. Smith: Computer Scientist
CRW - Chuck Watson: Director of NRA (National Radiobiology Archives)
RGT - Robert Thomas Glenn:
EKL - Earleen Ligotke: Archivist and clerk Preserves dog studies and documents
NAH - Nancy Holter: Computer Scientist
SDS - Shanna Schmidt: Administrative Specialist
James Newell Stannard* -
Ed Kidd* - (Director of ESTSC / Energy Science & Technology Software Center / Oak Ridge)
Philip C. Pulver (PNL)
Bill Morgan -
Tom Fritz -
James F. Park* - PI on Experiment 140
Cliff Burton - Database Administrator at LEHR
Charles Leonard Sanders (aka C.L. Sanders) (aka 'Chuck') - PNL/PNNL/Battelle Rodent Studies

* Deceased.

Timeline of experiments and major archive events

  • 1989 - Creation of the NRA
  • 1992 - ITRI files donated to the NRA. UC Davis Collection donated to PNL.
  • 1994 - Transfer of Information to the National Radiobiology Archives: In 1994, the records stored on the VAX computer were transferred to the PC environment and converted to PARADOX tables. This was part of the process of donating the information to the National Radiobiology Archives
  • 1994 - Morat.txt "DOE/RL announced today an indefinite moratorium on ADP equipment and furniture acquisition. This memo describes impacts of the moratorium on operation of the Health Risk Assessment Department (HRAD).
  • 1996 - The NRA program was transferred from Pacific Northwest National Laboratory (PNNL), operating for the U.S. Department of Energy, to the USTUR operations at WSU in 1996. The initial transfer included a limited collection of paraffin-embedded tissue blocks, microscope slides, clinical notes, pathologist observations, and several pieces of computer equipment. These specimens have been cataloged and are housed with the USTUR archives. Although the original archive collection at the NRA included formalin and/or alcohol-fixed tissues and thousands of radiographic films, concerns over the storage of such hazardous materials, coupled with budgetary constraints, led to proper disposal of these items which therefore were not transferred to the Registries with the other materials.
  • 2006 - PNL Materials transferred to USTUR as WSU.
  • 2010 - All materials associated with the NRA program were transferred to Northwestern University.
  • 2010 - "Beaglecon" happened in Richland, Washington in July of 2010. At this gathering, many key figures were present (Tom Fritz, Chuck Watson, etc.). This is where Ben was given data from Chuck Watson: it has been placed onto a 2.5" USB "Iomega" External Hard drive. There are also audio recording of this event (presumably taken by Ben), which Tanja mentioned she would like to have transcribed via software or service.

Beagle Data Congress

Todo

  • Unearth EasyCASE software. Open mystery files. SKS seems mostly responsible for leading the charge in using this software...
  • Maybe we want to have a chat with SKS?
  • Move vm to linux, automate .ps to .pdf print functionality.
  • Controls Database
  • Figure out what the deal is with Focus Hierarchical Database.

Unknown Terminology

Anything which is either partially understood or completely unknown should go here:

ANI - This is the name of a database table, however, maybe it stands for something. Knowing this could be useful...
AFIP - Possibly diagnosis codes used by UTAH, however, this is also an institution in and of itself. Possibly this: https://en.wikipedia.org/wiki/Armed_Forces_Institute_of_Pathology Needs confirmation...
RIB - Possibly Diagnosis codes similar to SNODOG???????? Possibly "Radioanalysis Inventory for Biology System Description"
PAL - Some manner of computer scripts. Also Object PAL.
IRDS - Information Resource Dictionary System. A horrible little acronym that says nothing about what it actually is.
RDM - NOT CLEAR. There is a reference in 960102/HISTO/README.TXT: "These files are intended for use by the RDM consultant." Any chance this could be related to Roelee? PNL_DOC.SAM also references "Walt developed a report procedure, named NRA, on his RDM database management system." NRA_U_CM.DTR suggests this is related to a Microvax in Utah "The input file is a report generated by RDM on the Utah micro VAX."

Queued questions for persons of interest

  • Possibly a question for Prof. G.B. Gerber, Mol, Belgium
    • Was RoeLee 84 used extensively? What was the nature of any data and does it still exist somewhere?

Lab Equipment and SOPs


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