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Verified Commit 6cdea300 authored by Marta Girona Alarcon's avatar Marta Girona Alarcon Committed by GitLab UZH
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modify mon_YYYY for YYYY_month and update tables

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webpage_contents/publications/20240901_Marta_GironaAlarcon/Input_mice_codebook.md
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- Metadata_file: Name of csv table with mice information
- Data_type: As labeled in metadata table column 'Data_type' and in the experiments page
- Facility_name_mon_YYYY: As labeled in the experiments the name should be that in the column 'Facility_name' of the page metadata table
- Facility_name_YYYY_month: As labeled in the experiments the name should be that in the column 'Facility_name' of the page metadata table
- SubjectID: Subject Identifier in the table
- Subject_pubID: Subject Identifier in the table
\ No newline at end of file
webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
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......@@ -22,42 +22,6 @@ code-fold: true
### Materials and equipment table
| Product number | Device | Reference | Company | State | Manufacturing country |
|----------------|---------------------------------------|----------------------------|----------------------------------|------------------|-----------------------|
| 1 | [ECG](https://cwe-inc.com/products/bioamplifiers/bma-200-single-channel-acdc-preamplifier) | BMA-200, NEE-3 | CWE Inc. | Pennsylvania | USA |
| 2 | [Small animal ventilator - hutch](https://cwe-inc.com/products/small-animal-ventilators/sar-1000-advanced-small-animal-ventilator) | SAR-1000 | CWE Inc. | Pennsylvania | USA |
| 3 | [Circulation thermostat pump - N/A - alternative water pump here](https://www.thermofisher.com/search/browse/category/ch/en/90088140?query=haake&focusarea=Circulating%20Baths) | Haake L / SAHARA PPO S5P | Thermo Fisher Scientific Inc. | Schwerte | Germany |
| 4 | [Flowmeter and gas mixer](https://cwe-inc.com/products/accessories/efm-4-flowmeterregulator-manifold) | EFM-4 | CWE Inc. | Pennsylvania | USA |
| 5 | [Data acquisition box, BNC-to-USB](https://digilent.com/shop/mcc-dt9800-series/) | DT9804 | Measurement Computing Corp. | Massachusetts | USA |
| 6 | [Tracheal cannula for mouse](https://www.hugo-sachs.de/tracheal-cannulae-with-y-adapter.html) | 73-2731 - OD 1.0 mm L 13 mm | Hugo Sachs Elektronik | March-Hugstetten | Germany |
| 7 | [Stereotaxic U-frame](https://www.rwdstco.com/product-item/standard-stereotaxic-instruments/) | SGL M digital 68801, 68665, 68202, 68207 | RWD Life Science Co. | Shenzen | China |
| 8 | Lateral ventricle fitting tube (#1) | C312VT vinyl - P1-8F027X045P01 | Bilaney Consultants GmbH | Düsseldorf | Germany |
| 9 | Lateral ventricle fitting tube (#2) | P50 Tygon | Access Technologies | Illinois | USA |
| 10 | Compression fitting 1 mm | HA-55750-01 | | | |
| 11 | 25 uL Hamilton syringe without needle | HA-80230 | BGB Analytik AG | Heidelberg | Germany |
| 12 | [Single syringe I/W nanoliter pump](https://www.rwdstco.com/product-item/syringe-pump-2/) | KDS Legato 130 | KD Scientific Inc | Holliston | USA |
| 13 | MRI microcannula | 328OP/PK/Spc 2.2, 2.3 or 2.5 mm | Bilaney Consultants GmbH | Düsseldorf | Germany |
| 14 | Dental drill | OmniDrill35 | World Precision Instruments GmbH | Friedberg | Germany |
| 15 | Health monitoring device PhysioSuite | PS-03,CBL-ANAOUT-MINI, E-RT-0002, E-RT-2-CUS, PS-05-module | Kent Scientific Corp. | Torrington | USA |
| 16 | ESRF camera | pco.edge 5.5 | PCO AG | Kelheim | Germany |
| 17 | Spring-8 camera | Hamamatsu ORCA-Flash4.0 | | | |
| 18 | Insulin syringe | Omnican 50 | Bbraun | | Switzerland |
| 19 | Cisterna magna fitting tube | Polyethylene 50 /23G | UNO | | |
| 20 | Cisterna magna metal clip | 00398-02 | Fine Scientific Tools Inc | Heidelberg | Germany |
| 21 | Tissue glue | VetBondTM 3M | | | |
| 22 | Anesthesia induction chamber | V-100-V | RWD Life Science Co. | | |
| 23 | Reptile temperature controller | ITC-308 WIFI | Inkbird Tech. C.L | Shenzen | China |
| 24 | Contrast agent | ExiTronTM nano12000 | ViscoverTM nanoPET Pharma GmbH | Berlin | Germany |
| 25 | Monitoring software LabChart | | ADInstruments | Dunedin | New Zealand |
| 26 | Monitoring software LabVIEW | | National Instruments | | |
| 27 | Wrap bandage - holder | KRUUSE Vet-Flex 5cm x 4.5m | Covetrus CH | Lyssach | Switzerland |
| 28 | Low-Profile Anesthesia mask Small | E-VETFLO-0801 | Kent Scientific Corp. | Torrington | USA |
| 29 | [Anesthesia induction chamber](https://www.rwdstco.com/product-item/anesthesia-induction-chambers/) | V100-V | RWD Life Science Co. | Shenzen | China |
| 30 | [Glue accelerator INSTA-SET](https://toni-clark-shop.com/INSTA-SET-Accelerator-56-ml) | GTIN 707336151009 | Toni Clark GmbH | Lübbecke | Germany |
| 31 | [Rodent warmer X1 with mouse heating pad](https://stoeltingco.com/Neuroscience/Rodent-Warmer-X1~10331?navigate_from_document=1013&navigated_from_object=3831) | 50304, 53800M, 53810 | Stoelting Co. | New York | USA |
| 32 | [Grooming clipper Aesculap Exacta](https://www.groomers-mall.ch/en/p/dog-grooming-clipper-aesculap-exacta-li-ion-gt416) | GT416 | Groomers Mall GmbH | Ebmatingen | Switzerland |
| 33 | [Small animal ventilator - surgery](https://www.hugo-sachs.de/minivent-ventilator-for-mice-model-845-single-animal-volume-controlled.html) | MiniVent - Model 845 | Hugo Sachs Elektronik | March-Hugstetten | Germany |
## Supplemental Results
......@@ -92,7 +56,7 @@ library(dplyr)
inputs <- read.csv(file = 'input_mice.csv')
# Use data type and facility information to find the path to the relevant protocols
folders <- unique(cbind(inputs$Data_type,inputs$Facility_name_mon_YYYY)) # find table's unique variations of experiment type and facility
folders <- unique(cbind(inputs$Data_type,inputs$Facility_name_YYYY_month)) # find table's unique variations of experiment type and facility
paths <- as.data.frame(file.path(apply(folders, 1, paste, collapse = .Platform$file.sep), 'protocols')) #put together the paths
colnames(paths) <- 'Protocols'
......@@ -114,7 +78,7 @@ library(dplyr)
# Take the relevant rows from the tables specified in inputs
data_used <- list()
for (i in 1:nrow(inputs)){
row_filepath <- file.path(here::here(), 'experiments',inputs$Data_type[i], inputs$Facility_name_mon_YYYY[i], "metadata_tables", inputs$Metadata_file[i])
row_filepath <- file.path(here::here(), 'experiments',inputs$Data_type[i], inputs$Facility_name_YYYY_month[i], "metadata_tables", inputs$Metadata_file[i])
data_used[[i]] <- read.csv(row_filepath) %>% filter(SubjectID == inputs$SubjectID[i]) # read table and filter subject
}
......
webpage_contents/publications/20240901_Marta_GironaAlarcon/input_mice.csv
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Metadata_file,Data_type,Facility_name_mon_YYYY,SubjectID,Subject_pubID
Metadata_file,Data_type,Facility_name_YYYY_month,SubjectID,Subject_pubID
Mouse_list_ESRF_November_2021.csv,synchrotron_microCT,ESRF_2021_November,Mouse19,Exp1
Mouse_list_ESRF_November_2021.csv,synchrotron_microCT,ESRF_2021_November,Mouse21,Exp2
Mouse_list_SPring-8_May_2023.csv,synchrotron_microCT,SPring-8_May_2023,JP28,Exp3
......
webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice.csv
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Metadata_file,Data_type,Facility_name_mon_YYYY,SubjectID,Subject_pubID
Mice_Information_SPring-8_20230508.csv,synchrotron_microCT,SPring-8_May_2023,JP28,exp1
Mice_Information_dummy.csv,synchrotron_microCT,ESRF_01_Jan_0000,JP23,exp2
Metadata_file,Data_type,Facility_name_YYYY_month,SubjectID,Subject_pubID
webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice_codebook.md
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View file @ 6cdea300
- Metadata_file: Name of csv table with mice information
- Data_type: As labeled in metadata table column 'Data_type' and in the experiments page
- Facility_name_mon_YYYY: As labeled in the experiments the name should be that in the column 'Facility_name' of the page metadata table
- Facility_name_YYYY_month: As labeled in the experiments the name should be that in the column 'Facility_name' of the page metadata table
- SubjectID: Subject Identifier in the table
- Subject_pubID: Subject Identifier in the table
\ No newline at end of file
webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
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View file @ 6cdea300
......@@ -55,7 +55,7 @@ library(dplyr)
inputs <- read.csv(file = 'input_mice.csv')
# Use data type and facility information to find the path to the relevant protocols
folders <- unique(cbind(inputs$Data_type,inputs$Facility_name_mon_YYYY)) # find table's unique variations of experiment type and facility
folders <- unique(cbind(inputs$Data_type,inputs$Facility_name_YYYY_month)) # find table's unique variations of experiment type and facility
paths <- as.data.frame(file.path(apply(folders, 1, paste, collapse = .Platform$file.sep), 'protocols')) #put together the paths
colnames(paths) <- 'Protocols'
......@@ -76,7 +76,7 @@ library(dplyr)
# Take the relevant rows from the tables specified in inputs
data_used <- list()
for (i in 1:nrow(inputs)){
row_filepath <- file.path(here::here(), 'experiments',inputs$Data_type[i], inputs$Facility_name_mon_YYYY[i], inputs$Metadata_file[i])
row_filepath <- file.path(here::here(), 'experiments',inputs$Data_type[i], inputs$Facility_name_YYYY_month[i], inputs$Metadata_file[i])
data_used[[i]] <- read.csv(row_filepath) %>% filter(SubjectID == inputs$SubjectID[i]) # read table and filter subject
}
......
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