# MEC Lab Manager Survival Guide
## Overview
Welcome to the MEC Lab Manager Survival Guide! This is your go-to resource for keeping lab operations smooth. We'll cover everything from experiments and equipment maintenance to training, purchasing, and workflow management. Use it to stay organized, troubleshoot issues, and keep the lab running efficiently.
This guide is **a living document**, update it as procedures change to keep lab operations running smoothly.

For questions, reach out to **Mikayla Newbrey: [[e-mail]](mailto:[e-mail])**.

## Broad Job Description & Goals
### Lab Technician
* Conduct lab work using existing protocols for ongoing projects in lab
* Conduct data and project management tasks for associated projects
* Research, test and develop new protocols in the lab
* Potentially conduct associated field work for sample collections
* Potentially conduct bioinformatics and data analyses for projects in lab

### Lab Manager
* Serve as point person for training new and/or continuing personnel in lab as appropriate
* Conduct maintenance on instruments
* Coordinate lab purchases for appropriate projects in lab
* Research and collate information on purchases for new equipment, etc for lab as needed
* Broader mentor-mentee/professional development

---

## Weekly Docs
Tracking these points each week isn’t just for staying organized. When you’re juggling multiple projects, priorities shift and some work gets put on hold. If there’s no clear record, picking a project back up weeks later can be slow and frustrating. A concise weekly update keeps the context fresh, makes it easier to restart stalled work, and ensures everyone’s on the same page.

- ### **Tech Doc**
- Top Things to track in the Tech Document:
- **Projected tasks**
- List out top priorities for coming week
- **Project status updates**
- Which experiments are in progress, on hold, or completed.
- **Pending purchases & reagent needs**
- Any key supplies missing to move forward.
- **Instrument usage & maintenance schedules**
- Ensuring equipment is available and properly calibrated.
- **Lab logistic logs**
- Notes on recurring lab issues and ongoing problem-solving.
- **Personnel assignments (Techs / UGs)**
- Who is working on what and when they will be available.

- ### **Timesheets**
- Submission deadlines and approval process
- ### **Weekly Check-Ins**
- Purpose and expectations
- Meeting frequency and agenda
- ### **Meeting Agenda**
- Purpose and expectations
- Meeting frequency and agenda

---
## Purchasing
### Ordering Through BuyWays
> To gain access to BuyWays you can follow [this protocol](https://docs.google.com/document/d/1LFYBHHmyMDeZgjwRoO1qwCLwZvAY9JC6/edit).

**[Access to BuyWays](https://www.umass.edu/afsystems/umass-buyways)**
#### **BuyWays Order Process**
- Steps to place an order
- Assigning the cart and follow-ups
- Contact for approvals: Daniel Warner
- [[e-mail]](mailto:[e-mail])
- **Shipping instructions**
- For any reagents or items requiring temperature control during shipment, always have them delivered to CEMS (Chemical Environmental Management System). CEMS inventories lab reagents and ensures temperature-sensitive items are stored properly upon arrival.
- **This is crucial**: If no one is available in the lab to receive the shipment, temperature-sensitive materials won’t be left sitting in the mailroom. Instead, they will be kept in a controlled environment, preserving their integrity until you retrieve them.
- The protocol above details the CEMS delivery address and when to specify this during your order placement.

- **Vendor & Supplies Management**
- Referencing the [supplies_and_purchases](https://docs.google.com/spreadsheets/d/1kBvdQF9G_C_dVRcnAQHUq-ZgL5cR9DPK/edit?gid=397812162#gid=397812162) document
- Managing bulk orders efficiently

### Local Regional Reps
> Sometimes, certain orders or services must be placed through local representatives rather than directly through BuyWays or a vendor’s website. Local reps can provide quotes, assist with bulk pricing, and help navigate product availability or delivery timelines. To request a quote, you can email the contacts below with details about the items you need to purchase.

| Vendor | Contact Person | Email |
| -------- | -------- | -------- |
| Rainin | Adam Vasellina | [e-mail] |
|Eppendorf| -------- | -------- |
| Takara Bio | Chris Hooper | [e-mail] |

❗️Keep in mind that these representatives and their contact information can change frequently, so be sure to update this list regularly to avoid delays.

---
## SciShield
**[Access to EH&S SciShield ]((https://ehs.umass.edu/cems-hazardous-material-inventory-management))**
### Waste Management
#### Handling and Disposal of Lab Waste
- SciShield enables labs to schedule hazardous waste pickups efficiently. Users can submit requests for waste collection, ensuring timely and compliant disposal.
#### Compliance and Safety Protocols
- The platform provides access to the university's Chemical Hygiene Plan and other safety guidelines, assisting labs in adhering to established protocols. It also offers training modules to keep lab personnel informed about safety procedures.
#### Reporting and Documentation Requirements
- Labs can maintain records of waste disposal activities within SciShield, facilitating easy retrieval during audits or inspections. The system also allows for incident reporting, ensuring that all safety-related events are documented appropriately.

### Chemical Inventory Management
#### Request Lab Supplies
- Order necessary supplies, including hazardous materials, through the platform.
#### Access Safety Data Sheets (SDS)
- Easily retrieve SDS for chemicals in the inventory, ensuring proper handling and emergency measures are understood.
#### Update Contact Information and Print Door Cards
- Maintain up-to-date lab contact details and generate door cards as needed.

### Personal Protective Equipment (PPE)
#### UMass Amherst Lab Coat Management Program
- The [UMass Amherst Lab Coat Management Program](https://ehs.umass.edu/lab-coat-management-program) ensures that researchers and students have access to properly fitting lab coats tailored to their specific laboratory hazards. The program also provides professional laundering services to maintain hygiene and safety standards.
##### Ordering Lab Coats
- To obtain a lab coat:
- Select a Pickup/Drop-off Location
- The closest location to our lab for both pickup and laundering services is Chenoweth 107.
- Choose the appropriate lab coat type based on lab safety requirements.
- Submit your request through the [Lab Coat Request Form](https://forms.office.com/Pages/ResponsePage.aspx?id=C4vQe5UzwU2Uu9Cy5WpJf9ETKZoXUhZMmbhy_JSiE2tUMzg1RkpYVVZOVVRWNVE5VE0wM1dQTThPOSQlQCN0PWcu).

##### Returning Lab Coats
If returning lab coats due to excessive wear or lab members leaving, follow these steps:
1. Email [e-mail] and provide the following information:
* Name on coat: (Provide name on coat)
* Barcode: (List barcode number)
* Building: Chenoweth 107
* Request for the coat to be removed from the lab’s inventory.
2. Drop off the coat in the designated laundering hamper at Chenoweth 107 (same location as laundering services).

By following these steps, lab coat inventory remains up to date, and worn-out coats are properly retired.

---
## Lab Sustainability
> Sustainability in the lab is essential for reducing waste, protecting equipment, and maintaining a safe and efficient workspace. Follow these best practices to minimize environmental impact and preserve lab resources.

### Food Waste
- Compost food scraps in the mailroom compost bin.
- DO NOT dispose of food waste (including wrappers, etc.) in the lab or bioinformatics room trash.
- **Why?** We are in an old building with ongoing rodent issues.
- Mice can:
- Chew through expensive equipment cords.
- Contaminate sterile supplies, ruining materials for molecular work.
- **Solution:** Use a carry-in, carry-out policy for food waste.

### Lab Consumable Recycling Stations
##### **We recycle plastics whenever possible.**
> Collection bins are available in the lab for proper sorting and disposal.
Always check that items are free of contaminants before placing them in recycling.

#### Beta Carbin – Clear Plastic Recycling

*Which pipette tips can be recycled?*
- All used pipette tips (**excluding those from post-PCR work**) should be placed in the tip disposal container inside the fume hood.
- **Why?** This allows residual liquids to properly evaporate, preventing contamination before they are moved to recycling.
- **Final disposal steps:**
- Once completely dry, transfer the pipette tips into the clear plastic recycling bin.
- For Post-PCR work, leave tips in the containers overnight and dispose of them in the recycling bin the following day
- Bins designated for pipette tip recycling must be **lined with a clear plastic bag**.

**Tip Boxes & Components**
- Tip boxes must be disassembled before disposal.
- Clear Lids should be neatly stacked inside the recycling bin to optimize space.

#### Alpha Carbin – Tip Box Recycling
- DO NOT throw away empty TipOne or Rainin refillable tip boxes.
- Once empty, remove the wafer from the tip box and save it for refilling.
- Once other non-refillable tip boxes are empty:
1. Remove the wafer and place it in the designated tip wafer box (for moving PCR from pre to the thermocycler).
2. Place the empty tip box in the Alpha Carbin recycling bin.

#### Gamma Carbin – Nitrile Glove Recycling
> We participate in a nitrile glove recycling program to reduce waste.

- How to recycle gloves properly:
1. Only clean, uncontaminated nitrile gloves can be recycled.
2. Used gloves should be collected in the Gamma Carbin bin designated for nitrile glove recycling.

#### Returning Recycling to Polycarbin
When the bin is full, it will be processed for recycling rather than sent to landfill.

### Other Recycling Stations
- Paper & plastic/can recycling is located in the lab.
- Styrofoam recycling is available upstairs in Holdsworth by leaving the styrofoam by the dock near the custodial office on the 1st floor.
- Terra-racks (pipette tip racks) go into the regular recycling stream.
- *good* Plastic bags should be saved and stored in the designated "Plastic Bags" box on the field supplies shelf.

#### **Misc Recycling (e.g., empty reagent containers)**

- For Small Reagent Containers:
- Rinse thoroughly (*at least 3 times or until completely clean*) before placing in recycling.
- Ensure [Chemical Inventory barcode](https://hackmd.io/_rimGykPRIOeSHWPcC566A?both#%F0%9F%A7%AA-SciShield) is saved
- Remove other labels if possible.

- For Large Containers (e.g., Bleach & Ethanol Bottles):
- After rinsing, place in the fume hood to allow any remaining residue to evaporate.
- Do NOT discard immediately—these containers should be saved for designated waste disposal streams.
- Once completely dry, follow lab waste disposal guidelines or repurpose as appropriate.

#### Reusable Items & Single-Use Plastic Reduction:
- Leave mugs/utensils in the lunchroom to cut down on disposable plastic use.
- Wash all items before leaving for the day to avoid attracting mice.

---
## Equipment Maintenance
### Fragment Analyzer
> The Fragment Analyzer is used for high-resolution separation of nucleic acids. Keeping it calibrated and clean ensures accurate results.

### Pipette Calibration
> Proper pipette calibration ensures accuracy and reproducibility in experiments. Check Pipettes for their last calibration date and make note of any pipettes that may be acting up.

### All Fridges & Freezers
> Our freezers store critical (*sometimes irreplaceable*) biological samples and reagents. Regular maintenance and checks prevents temperature fluctuations that could cost us thousands of dollars to lost experiments.

- Inspect door seals and gaskets for wear
- **Why?** Worn-out seals are a major cause of temperature fluctuations and frost buildup.
- **How?** Check for visible cracks, gaps, or looseness.
- If seals are damaged, let Lisa know and look into possible options for replacement.
- Ensure doors are fully sealed and no frost buildup is occurring
- If frost is accumulating, verify that the doors are closing properly.
- **Never leave doors slightly ajar**, even for a minute, as this leads to rapid ice buildup and temperature fluctuations.
- Check for ice buildup
- If ice accumulates beyond normal levels, discuss with Lisa to schedule a defrosting plan.
- During defrosting:
- Transfer critical samples to backup freezers.
- Monitor temperature changes closely.
- Relocate all reagents & critical samples during maintenance
- Plan ahead and use backup storage solutions to avoid sample degradation.
- Use temperature loggers if needed to track exposure during transfers.

#### -80º Freezer
##### Backup Battery
- Ensure backup power supply is functional.
- The -80º freezer has a backup battery supply from a **SigmasTek Battery, SP12-12 (12V12AH/T2)**.
- If the backup battery supply runs low, it will beep insesently. Order a new battery ASAP and contact facilities to schedule them to change out the battery.
- This is a very easy swap; essentially like changing a lawn mower battery. In the past Marc Duzsca has taken care of this for us
- The last time the backup battery was changed was January 28th, 2025. Hampshire Controls’ Tech service mentioned that the batteries last ~4 years.
##### Carbon Dioxide (CO₂) Backup
- Hookup: Connected to a CO₂ cylinder via an insulated supply line and automatic injection system.
- Usage: CO₂ is injected into the freezer when temperatures exceed the critical range.
- Check gas levels regularly to ensure backup supply is adequate.
- Inspect fittings and hoses monthly for leaks or frost buildup.
- Test the emergency activation system at least once per year.

#### -20º Freezers
##### -20º in Pre

##### -20º in Post

---

### Emergency Protocol
If any fridges or freezers experience unexpected temperature changes or failure, **call Lisa immediately**.

#### In Case of Power Failure:

#### Do NOT open any freezers or fridges.
Keeping the doors sealed will help maintain the internal temperature for as long as possible.

#### Immediate Actions:

##### Step 1: Confirm the power outage.
- Check if the outage is affecting the whole lab/building or just specific equipment.
- If isolated, check the circuit breakers and power connections.

##### Step 2: Explore a secondary power source.
- If the power failure is prolonged, a generator should be secured to maintain freezer function.
- Coordinate with Lisa or facilities to determine backup power availability.

##### Step 3: Monitor temperatures remotely (-80º).
- The -80º has an external monitoring system and battery backup for temperature tracking, use it to assess stability.

##### Step 4: Prepare for potential sample transfer.
- If power is not restored within a critical timeframe, prepare to move samples to backup freezers in another facility (**only if absolutely necessary**).
- Use dry ice or liquid nitrogen storage if no other options are available.

##### Step 5: Contact Facilities for emergency response.
- If power is not restored promptly, escalate to building management and coordinate with Lisa and Facilities for long-term solutions.

---
## End-of-Day Walkthrough

> As a lab manager, you won’t always be the last one to leave the lab, but more often than not, you will find yourself in that position. Regardless, it is crucial to ensure a proper end-of-day walkthrough to maintain lab safety, equipment functionality, and overall organization. If you are not the last one out, make sure to ask whoever is lingering to handle the final walkthrough.

### Steps for the Walkthrough

#### Check Sensitive Equipment

**Freezers and refrigerators**
- Ensure all doors are fully closed and that the temperatures are within acceptable ranges. If there are alarms or unexpected fluctuations, investigate and address them accordingly.

**Thermocyclers**
- Ideally, turn them off unless a cycle is actively running.
- If a cycle is still in progress, verify the expected completion time and make sure it isnt going to be on through the weekend.

**Centrifuges**
- Ensure lids are closed, and the machines are off unless actively in use.

**Nanopore and Sequencing Equipment**
- Confirm that any ongoing runs are progressing as expected, and check for potential errors or alerts.

#### Check General Lab Safety and Cleanliness

- Ensure that all hazardous materials and biological samples are properly stored.
- Confirm that chemical fume hoods and biosafety cabinets are turned off or in the proper operational state.
- Turn off unnecessary lights and power-consuming equipment.

#### Waste Disposal
- Dispose of chemical waste properly or ensure it is stored in designated areas.
- **Remove any perishable items from benchtops and sinks.**
- If it is suspected someone leftthis out make sure you let them know

#### Final Check and Lock-Up

- Verify that all doors and windows are securely locked.

📌 A thorough walkthrough at the end of the day helps prevent accidents, equipment malfunctions, and unnecessary stress.

---
## Physical Plant / Facilities Work Orders
> We work in an old building that has recurring issues with leaks, ceiling debris, Malfunctioning equipment (e.g., fume hood controls).
> To protect lab equipment and prevent sample loss, stay observant and report any issues ASAP.

### How to Report Issues
If you notice anything unusual, even if minor, report it immediately to Lisa.
- Use the best contact method based on severity:
- Slack (for general updates)
- Cell/Text (for urgent issues)
- WhatsApp group message (for emergencies)

⚡ Early detection is key, small problems can escalate quickly!
### Submitting a Work Order

### Surplus Equipment Disposal
---
## Weekly Chores

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## Project Management
> Effective project management ensures that experiments remain organized, reproducible, and easy to resume even after long pauses. Keeping detailed records helps prevent wasted time and resources.
### Maintain Lab Notebooks
- Clearly document methods, results, and any protocol adjustments made during experiments.
- Record dates, sample IDs, reagent lot numbers, and any anomalies to ensure reproducibility.
- Document protocol changes and share with the team.

### Document Protocol Changes
- If you modify an existing protocol, update the shared lab protocol document and notify the team.
- Include a brief note in your lab notebook explaining the rationale for any changes.

### Track Project Status
- Regularly update the Tech Doc so that project progress is easily accessible.
- If troubleshooting issues, document failed runs, suspected causes, and potential solutions in a [read.me](https://www.makeareadme.com/) doc for the project and link that to the Tech Doc.

📌 **Pro Tip:** If you feel like you may step away from a project for a while, always write a short summary of where you left off. Your future self will thank you when you need to pick it back up!

---
## Data Management
> Effective data management is critical for research success, ensuring accessibility, reproducibility, and compliance with funding requirements. Well-organized data saves time, supports collaborations, and is often required for grant proposals.

### Organizing and Storing Data
#### Create a Data Management Plan (DMP)
- Standardize data collection, processing, verification, and archiving methods.
- Use the Great Origins Document: A Guide to Data Management in Ecology and Evolution (found in the Lab Resources Folder) as a reference.
- Ensure a README file is included in every project folder, explaining data structure, naming conventions, and key details.

### Data Storage & Backups
**All raw files must be saved in a minimum of two locations**

#### Primary storage options:
- Google Drive (preferred cloud storage at UMass Amherst)
- MEC Data Archive (lab-specific storage space for permanent datasets)

#### Backup options:
- External hard drives (for local, offline storage)
- Automated cloud syncing via Google File Stream for continuous backups

#### Backup Frequency:
- If using Google Drive → Enable auto-backup through Google File Stream.
- If using an external hard drive → Set reminders for regular data backups.
- For physical documents or handwritten notes → Scan and store a digital copy in the appropriate cloud drive folder.

### Key Takeaways for MEC Lab Data Management
1. Always maintain a README file for every project.
2. Use a consistent directory structure and naming conventions.
3. Backup all data in at least two locations (Google Drive & external storage).
4. Run checksums on data to prevent corruption.
5. Use non-proprietary formats for maximum accessibility.
6. Clean up unnecessary files regularly to avoid exceeding storage limits.
7. Document analyses in HackMD and store scripts on GitHub.

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## Onboarding / Offboarding New Lab Members
- **Onboarding**
- Setting up SciShield access
- Required training and documentation
- Lab safety protocols
- **Offboarding**
- Returning lab materials
- Account deactivation process
- Final checklist before exit

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