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diff --git a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Input_mice_codebook.md b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Input_mice_codebook.md
index bcdb4abc184df716d11a1385853fc4f6536e4fbd..5b43b000c94cef44c2f836f3097fda29c87fc850 100644
--- a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Input_mice_codebook.md
+++ b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Input_mice_codebook.md
@@ -1,5 +1,5 @@
- 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
diff --git a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
index 29c2ec55e93d7ca2eff3d67b38192b226215aa8d..2108d7afbba8b4c9ba55606c91670717debba131 100644
--- a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
+++ b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
@@ -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
}
diff --git a/webpage_contents/publications/20240901_Marta_GironaAlarcon/input_mice.csv b/webpage_contents/publications/20240901_Marta_GironaAlarcon/input_mice.csv
index 1e39e1f1282fc285a5446838f3e0fbf93450ac66..e5169cecc65f4e53ba3a7d239ff7f3e6d07dcd9e 100644
--- a/webpage_contents/publications/20240901_Marta_GironaAlarcon/input_mice.csv
+++ b/webpage_contents/publications/20240901_Marta_GironaAlarcon/input_mice.csv
@@ -1,4 +1,4 @@
-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
diff --git a/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_YYYY_Month.xlsx b/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_YYYY_Month.xlsx
deleted file mode 100644
index 4cb608772b54afbb4083f96100e30cac0599a388..0000000000000000000000000000000000000000
Binary files a/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_YYYY_Month.xlsx and /dev/null differ
diff --git a/webpage_contents/experiments/synchrotron_microCT/CLS_2023_November/metadata_tables/xlsx/Mouse_list_Facility_YYYY_Month.xlsx b/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_YYYY_month.xlsx
similarity index 100%
rename from webpage_contents/experiments/synchrotron_microCT/CLS_2023_November/metadata_tables/xlsx/Mouse_list_Facility_YYYY_Month.xlsx
rename to webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_YYYY_month.xlsx
diff --git a/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_month_YYYY.xlsx b/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_month_YYYY.xlsx
deleted file mode 100644
index dda725582addc241b15e7585a3de7ccbb2a35b3a..0000000000000000000000000000000000000000
Binary files a/webpage_contents/templates/templates_for_experiments/Facility_YYYY_month/metadata_tables/xlsx/Mouse_list_Facility_month_YYYY.xlsx and /dev/null differ
diff --git a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice.csv b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice.csv
index d2af8bda5b6277a72aae74e5f269d03d138cb4c3..9d78a4c374cd25dce38f4f48f601bfbb7bc1f76e 100644
--- a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice.csv
+++ b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice.csv
@@ -1,3 +1,2 @@
-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
+
diff --git a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice_codebook.md b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice_codebook.md
index bcdb4abc184df716d11a1385853fc4f6536e4fbd..5b43b000c94cef44c2f836f3097fda29c87fc850 100644
--- a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice_codebook.md
+++ b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Input_mice_codebook.md
@@ -1,5 +1,5 @@
- 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
diff --git a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
index d9731b143d55a2926f10043bd858cffb375d791b..dbb0d612d591c9aefad27d564a9120407360c923 100644
--- a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
+++ b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
@@ -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
}