Adding reagent contribution shortcut example.

docs/reagent_contribution_shortcut/README.md

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+
+
+# Reagent Contribution Shortcut Instructions
+
+Welcome to the reagent contribution shortcut, where we work together to enable you to easily add reagent information to the Knowledge-Base. You provide the scientific information, and we take care of the technical parts (git, GitHub, formatting).
+
+Please read the general [contribution instructions](../contrib.md) before proceeding. Primarily, familiarize yourself with the expected supporting image conventions if you intend to provide supporting images.
+
+You will need to provide us with the following:
+1. A csv with the columns listed in [this example](new_entries.csv). This csv is similar to the one used by the Knowledge-Base and contains two additional columns, `Publications`,and `Notes`.
+2. `Publications` column - If there are one or more publications associated with a reagent validation, list each one in a markdown file [like this one](pub1.md) and reference them in this column (file names are separated by a semicolon). If there are no publications, leave the column entry empty.
+3. `Notes` column - If there are notes that you would like to provide, information that is not listed in any of the columns, this is where to provide it. For example "This alpha smooth muscle actin antibody labels cytoskeleton proteins in various mouse tissues. In the tumor, the AF488 conjugate (53-9760-82) works very well and labels actin family of proteins, smooth muscle cells, and cancer associated fibroblasts." If there are no notes, leave the column entry empty.
+4. `Image Files` column - If you have one or more images that support the specific validation, list them in this column (file names are separated by a semicolon). Note that the same file may support multiple validations and we only keep a single copy of it. Consequentially, you will need to decide in which directory (`target_conjugate` directory name) you want the image to reside. In the [example](new_entries.csv) we have two image files and both will reside under a directory `BCL2_Unconjugated`.
+
+Finally, provide the image files in a single directory. Use meaningful image file names similar to those provided in the [example directory](images).

docs/reagent_contribution_shortcut/new_entries.csv

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+UniProt Accession Number,Reagent Type,Target Name / Protein Biomarker,Target Species,Host Organism,Isotype,Clonality,Vendor,Catalog Number,Conjugate,RRID,Availability,Method,Tissue Preservation,Target Tissue,Tissue State,Detergent,Antigen Retrieval Conditions,Dye Inactivation Conditions,Recommend,Agree,Disagree,Contributor,Image Files,Captions,MD5,Publications,Notes
+P10415,Primary Antibody,BCL2,Human,Rabbit,IgG,SP66,Abcam,ab236221,Unconjugated,NA,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,Pay attention to this and pay attention to that.
+P10415,Primary Antibody,BCL2,Human,Rabbit,IgG,SP66,Abcam,ab236221,Unconjugated,NA,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human FL LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,Pay attention to this and pay attention to that.
+P07766,Primary Antibody,CD3,Human,Rabbit,IgG,EP4426,Abcam,ab208514,AF555,AB_443425,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,
+P07766,Primary Antibody,CD3,Human,Rabbit,IgG,EP4426,Abcam,ab208514,AF555,AB_443425,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human FL LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,
+P01730,Primary Antibody,CD4,Human,Rabbit,IgG,EPR6855,Abcam,ab196372,AF488,AB_2889191,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,
+P01730,Primary Antibody,CD4,Human,Rabbit,IgG,EPR6855,Abcam,ab196372,AF488,AB_2889191,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human FL LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,
+P20023,Primary Antibody,CD21,Human,Rabbit,IgG,SP186,Abcam,ab306325,PE,NA,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967,BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg,"Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325)",,pub1;pub2,Note about CD21.

docs/reagent_contribution_shortcut/pub1.md

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+A. J. Radtke et al., "Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients", Cancer Cell, 42(3):444-463, 2024, [doi: 10.1016/j.ccell.2024.02.001](https://doi.org/10.1016/j.ccell.2024.02.001).

docs/reagent_contribution_shortcut/pub2.md

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+A. J. Radtke et al., "A Multi-scale, Multiomic Atlas of Human Normal and Follicular Lymphoma Lymph Nodes", *bioRxiv*, 2022, [doi: 10.1101/2022.06.03.494716](https://doi.org/10.1101/2022.06.03.494716).

docs_in/contrib.md.in

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 ⚠ **NOTES**
 * By contributing to the knowledge-base you are agreeing that the provided data be made available under a [Creative Commons Attribution 4.0 International license](https://creativecommons.org/licenses/by/4.0/) and that you will abide by the [code of conduct](code_of_conduct.md) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.html).
-* The recommended path for contributing is described below and utilizes the git version control system and the GitHub repository hosting service. If you feel uncomfortable using either of these tools, we will help you contribute your knowledge without dealing with them. Download the knowledge-base as a [zip file](https://github.com/IBEXImagingCommunity/ibex_imaging_knowledge_base/archive/refs/heads/main.zip), read the instructions below, skipping the git and GitHub related steps. [Contact us](mailto:zivyaniv@nih.gov,andrea.radtke@leica-microsystems.com) so that we can discuss your contribution and help you complete the submission together.  
+* The recommended path for contributing is described below and utilizes the git version control system and the GitHub repository hosting service. If you feel uncomfortable using either of these tools, we will help you contribute your knowledge without dealing with them. Download the knowledge-base as a [zip file](https://github.com/IBEXImagingCommunity/ibex_imaging_knowledge_base/archive/refs/heads/main.zip), read the instructions below, skipping the git and GitHub related steps. [Contact us](mailto:zivyaniv@nih.gov,andrea.radtke@leica-microsystems.com) so that we can discuss your contribution and help you complete the submission together. If you are contributing new reagent validations see the [shortcut instructions](reagent_contribution_shortcut/README.md).  
 Before going down this route, we highly recommend reading the following publications [Pereira Braga et al. 2023](https://doi.org/10.1111/2041-210X.14108) and [Chen et al. 2025](https://doi.org/10.1371/journal.pbio.3003029). They may just convince you to learn how to use GitHub, as they show it is a useful tool for general laboratory research and that it has the potential to accelerate research while improving reproducibility.
 * If you are comfortable with Python, code for validating the contributions, converting data files to markdown and easily creating supporting material is available [here](https://github.com/IBEXImagingCommunity/ibex_imaging_knowledge_base_utilities).