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docker-compose.yml

Millar group

With this file the user can type

docker-compose up

and will be able to run the operating system were the modelling and analysis took place

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Recalibrating the clock models for absolute pro...

Assays: Reproducibility tool set

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Created: 20th Oct 2024 at 18:06, Last updated: 19th Dec 2024 at 11:29

Jupyter notebook for Protein predictions and U2019.4 rescaling

Millar group

The jupyter notebook contains the code that predicts the number of monomers of several clock proteins and rescales the U2019.4 model which was published https://doi.org/10.1093/insilicoplants/diab022

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Predicting absolute levels of clock proteins wi...

Assays: Jupyter notebook Predicting Protein Numbers

Download

Created: 15th Jan 2023 at 10:03, Last updated: 19th Dec 2024 at 11:29

scaling factors for U2019.4 and predicted protein from timet

Millar group

This file contains the scaling factors that can be used with U2019.4 that will match synthetic protein data generated with the simple translation model.

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Predicting absolute levels of clock proteins wi...

Assays: Jupyter notebook Predicting Protein Numbers

Download

Created: 15th Jan 2023 at 10:13, Last updated: 19th Dec 2024 at 11:29

Jupyter notebook for Protein predictions and U2020.4 rescaling

Millar group

The jupyter notebook contains the code that predicts the number of monomers of several clock proteins and rescales the U2019.4 model which was published https://doi.org/10.1093/insilicoplants/diab022

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Predicting absolute levels of clock proteins wi...

Assays: Jupyter notebook Predicting Protein Numbers

Download

Created: 2nd Apr 2023 at 16:01, Last updated: 19th Dec 2024 at 11:29

U2019.4 equations in PDF

Millar group

PDF of U2019.4 equations

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Predicting absolute levels of clock proteins wi...

Assays: Jupyter notebook Predicting Protein Numbers

Download

Created: 8th Apr 2023 at 18:56, Last updated: 19th Dec 2024 at 11:29

U2020.4 equations in PDF

Millar group

PDF of U2020.4 equations

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Predicting absolute levels of clock proteins wi...

Assays: Jupyter notebook Predicting Protein Numbers

Download

Created: 9th Apr 2023 at 06:36, Last updated: 19th Dec 2024 at 11:29

Linking U2019.5 and U2020.5 to protein data in absolute number of molecules per cell

Millar group

Jupyter notebook file that describes how the models were finally linked to produce several plots were model predictions and data are compared

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Investigations: Absolute units for proteins in Arabidopsis cloc...

Studies: Predicting absolute levels of clock proteins wi...

Assays: Jupyter notebook Predicting Protein Numbers

Download

Created: 27th Aug 2024 at 08:22, Last updated: 19th Dec 2024 at 11:29

The role of different fatty acids

No description specified

Creator: Fengming Xu

Submitter: Fengming Xu

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 12th Nov 2024 at 15:37

protocols/Methods Fungi extraction_T33.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T33_MonoterpenoidsFungi

Studies: Investigation files

Assays: _I_T33_MonoterpenoidsFungi-files

Download

Created: 18th May 2022 at 09:44, Last updated: 7th Nov 2024 at 10:06

protocols/Methods GC-MSMS_T33.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T33_MonoterpenoidsFungi

Studies: Investigation files

Assays: _I_T33_MonoterpenoidsFungi-files

Download

Created: 18th May 2022 at 09:44, Last updated: 7th Nov 2024 at 10:06

output/raw/README.MD

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_liq-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T33_MonoterpenoidsFungi

Studies: _S_P5_SxF_lav_ac

Assays: _A_LA_liq-GC-MS

Download

Created: 18th May 2022 at 09:45, Last updated: 7th Nov 2024 at 10:06

output/raw/README.MD

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T33_MonoterpenoidsFungi

Studies: _S_P5_SxF_lav_ac

Assays: _A_LA_myc-GC-MS

Download

Created: 18th May 2022 at 09:46, Last updated: 7th Nov 2024 at 10:06

output/raw/README.MD

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T33_MonoterpenoidsFungi

Studies: _S_P5_SxF_lavandulol

Assays: _A_L_liq-GC-MS

Download

Created: 18th May 2022 at 09:46, Last updated: 7th Nov 2024 at 10:06

output/raw/README.MD

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T33_MonoterpenoidsFungi

Studies: _S_P5_SxF_lavandulol

Assays: _A_L_myc-GC-MS

Download

Created: 18th May 2022 at 09:46, Last updated: 7th Nov 2024 at 10:06

reports/QuantificationsTransientLPPSCPPS.pptx

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T32_CandidateGeneExpressionTesting

Studies: _S_TransientLPPSCPPS

Assays: _S_TransientLPPSCPPS-files

Download

Created: 17th May 2022 at 14:16, Last updated: 7th Nov 2024 at 10:05

reports/QuantificationsTransientLPPSCPPS.pptx

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/_A_TransientCompLPPSCPPS-GCMS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T32_CandidateGeneExpressionTesting

Studies: _S_TransientLPPSCPPS

Assays: _A_TransientCompLPPSCPPS-GCMS

Download

Created: 17th May 2022 at 14:16, Last updated: 7th Nov 2024 at 10:05

output/raw/README.MD

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/_A_TransientCompLPPSCPPS-GCMS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T32_CandidateGeneExpressionTesting

Studies: _S_TransientLPPSCPPS

Assays: _A_TransientCompLPPSCPPS-GCMS

Download

Created: 17th May 2022 at 14:16, Last updated: 7th Nov 2024 at 10:05

output/raw/210311 vlc 4.aspk

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_EAGresponse

Assays: _A_GC-MS-EAD-EAG

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/210311 vlc 5.aspk

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_EAGresponse

Assays: _A_GC-MS-EAD-EAG

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/raw.zip

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr20-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_PhContentPlants

Assays: _A_PhCont_fr20-GC-MS

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/210115 SxP M1 b.raw

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr80-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_PhContentPlants

Assays: _A_PhCont_fr80-GC-MS

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/210115 SxP M2 b.raw

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr80-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_PhContentPlants

Assays: _A_PhCont_fr80-GC-MS

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/raw.zip

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fresh-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_PhContentPlants

Assays: _A_PhCont_fresh-GC-MS

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/raw.zip

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhEmissionPlants/_A_emission_nontruncated-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_PhEmissionPlants

Assays: _A_emission_nontruncated-GC-MS

Download

Created: 12th Apr 2022 at 16:20, Last updated: 7th Nov 2024 at 10:05

output/raw/raw.zip

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhEmissionPlants/_A_emission_truncated-GC-MS/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_PhEmissionPlants

Assays: _A_emission_truncated-GC-MS

Download

Created: 12th Apr 2022 at 16:21, Last updated: 7th Nov 2024 at 10:05

reports/Susphire Task 2.4_November 2020_Quarantine meeting.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: Investigation files

Assays: _I_T24_phero-files

Download

Created: 12th Apr 2022 at 16:17, Last updated: 7th Nov 2024 at 10:05

reports/210223 vlc 4.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_EAG_manual-EAG/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_EAGresponse

Assays: _A_EAG_manual-EAG

Download

Created: 12th Apr 2022 at 16:19, Last updated: 7th Nov 2024 at 10:05

reports/210226 vlc 2.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_EAG_manual-EAG/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_EAGresponse

Assays: _A_EAG_manual-EAG

Download

Created: 12th Apr 2022 at 16:19, Last updated: 7th Nov 2024 at 10:05

reports/210301 vlc 2.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_EAG_manual-EAG/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_EAGresponse

Assays: _A_EAG_manual-EAG

Download

Created: 12th Apr 2022 at 16:19, Last updated: 7th Nov 2024 at 10:05

reports/210311 vlc 3 vert.pdf

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/

Creator: Marko Petek

Submitter: Marko Petek

Investigations: _I_T24_phero

Studies: _S_P5_EAGresponse

Assays: _A_GC-MS-EAD-EAG

Download

Created: 12th Apr 2022 at 16:19, Last updated: 7th Nov 2024 at 10:05

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