# Research Data Management Guides — De Moraes/Mescher Laboratory

## About the Lab

The Biocommunication Group at ETH Zurich is part of the Department of Environmental Systems Science (D-USYS) and the Institute of Agricultural Sciences (IAS). Our research investigates the role of chemical signaling in ecological interactions, spanning tritrophic plant-herbivore-predator dynamics, plant responses to microbial and olfactory cues, plant-pollinator communication, and the ecology of vector-borne diseases. We combine approaches from molecular biology, analytical chemistry, behavioural studies, and field ecology.

## About These Guides

These guides support consistent, reproducible, and FAIR data management practices across the group. All incoming lab members — PhD students, postdoctoral researchers, and research staff — are required to follow these workflows as part of their onboarding. Our aim is to ensure research data remain well-organized, accessible to collaborators, and compliant with ETH Zurich open research data policy (RSETHZ 414.2).

Guides were prepared by Hannier Pulido (Data Manager, hannier.pulido@usys.ethz.ch).

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## Guide List

| File | Topic | Version |
|------|-------|---------|
| `ELN_Documentation_Guide_Biocomm_20260626.pdf` | How to create and document projects, experiments, and experimental steps in OpenBIS (ELN/LIMS) | v.20260626 |
| `FolderStructure_Documentation_Guide_Biocomm_20260626.pdf` | Folder structure and file naming conventions on the shared NAS drive | v.20260626 |
| `DataDeposition_Guide_Biocomm_20260626.pdf` | Active data storage rules, data flow to publication, and how to deposit projects to the lab GitLab repository | v.20260626 |
| `QRLabel_Printing_Guide_Biocomm_20260626.pdf` | Step-by-step workflow for generating and printing QR code labels for physical samples | v.20260626 |
| `GitLab_Workflow_Guide_Biocomm_20260626.pdf` | Git Bash setup, personal access tokens, cloning, committing, pushing, collaborating, and Zenodo DOI archiving | v.20260626 |
| `PermID_Handling_Guide_Biocomm_20260626.pdf` | What PermIDs are in OpenBIS, how to export them, and how to link physical samples to digital records | v.20260626 |
| `README_Template_Guide_Biocomm_20260626.pdf` | How to write a project README, required sections, fill-in template, and examples for different data types | v.20260626 |
| `Offboarding_Checklist_Biocomm_20260626.pdf` | Checklist for departing lab members covering ELN handover, NAS organisation, GitLab, physical samples, and knowledge transfer | v.20260626 |

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## Lab Infrastructure

| System | Purpose | Access |
|--------|---------|--------|
| OpenBIS ELN/LIMS | Electronic lab notebook and sample management | openbis-biocommunication.ethz.ch |
| Shared NAS drive | Active project storage (mandatory for all data) | P:/ (mapped network drive) |
| GitLab repository | Code and data deposition for publications | gitlab.ethz.ch/biocommunication |
| Zenodo | Permanent archiving and DOI issuance for published datasets | zenodo.org |

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## Key Rules

- **All data must be stored on the shared NAS** (P:/). Personal computers and local drives are not permitted as primary storage.
- **Every project must be documented in OpenBIS** with an experimental step for each experiment, linked to physical samples via QR/PermID labels.
- **All code and processed data underlying a publication must be deposited** to the lab GitLab before submission, and archived to Zenodo to obtain a DOI.
- **Every project folder on the NAS must contain a README.md** describing the contents, data columns, methods, and software versions.
- **Departing lab members must complete the Offboarding Checklist** and have it signed off by the data manager before their last day.

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## Contact

**Hannier Pulido** — Data Manager
ETH Zürich, D-USYS
hannier.pulido@usys.ethz.ch

This training material is Module 5 of 5 of the training series by the EPFL Library Research Data team. It focuses on data and code publication, including why data and code should be treated as academic outputs, how to choose appropriate repositories, how to distinguish sharing from publication, how to use persistent identifiers and metadata to support FAIR and reusable outputs, and how to select suitable licenses for datasets and code. It also introduces practical publication workflows commonly used at EPFL, including Zenodo, the EPFL Zenodo community, the connection between Zenodo and GitHub, data journals, data availability statements, and key constraints related to privacy, third-party rights, commercialization, and potential valorization.

Designed for an instructor-led online or onsite workshop (~90 min, introductory level), it is published as an Open Educational Resource (OER). The package includes slides (.pptx and .odp with some speaker notes), a static .pdf export, a dataset for publication exercise (.csv) with its own README, and a README for this training module.

Here are the OER related to the five modules:
Module 1: Training "ABC of Research Data Management (RDM)"
Module 2: Training "Data Management Planning & Funding"
Module 3: Training "Data Organization & Storage Solutions"
Module 4: Training "Ethics in Research Data Management: Anonymization and Best Practices"
Module 5: Training "Data/Code Publication"