Laboratory and Data Management for Scientists. David L. Blum, Ph.D. Research Assistant Professor Department of Biochemistry
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1 Laboratory and Data Management for Scientists David L. Blum, Ph.D. Research Assistant Professor Department of Biochemistry
2 OUTLINE Project Management Choosing the right project Project Plans Project Management tools Data Management Record Keeping Inventory Number crunching
3 Project Management
4 Choosing the right project Be publication oriented Keep goals/deliverables in mind Have a timeline, but be flexible Make sure key materials/resources are available Access to samples Capital equipment
5 Statement of Work Purpose Background Scope of Work Objectives Statement Measures Specifications Constraints Limitations Needs Assumptions
6 Audience - People affecting the success of your project Drivers - you, collaborators, editors Supporters - lab personnel Observers - colleagues
7 Project Plans To Gantt or not to Gantt? Critical Paths Deadlines (real or imaginary?) Milestones Activities Plan Events Schedule Things not under your control Plan for the worst hope for the best
8 GANTT charts Developed by Karol Adamiecki and published by Henry Gantt in 1910 (Harmonogram)* Allows users to map out project timelines and show dependency of tasks PERT (Program Evaluation and Review Technique) is another type of project management tool. Activities represented by interconnected lines and nodes instead of horizontal lines (GANTT) *
9 GANTT Chart Definitions Task - An action in a project plan Link - a way to visually show a connection between 2 adjacent tasks Critical Path - sequence of events denoted the minimum time to complete a project Milestone - event marking a significant change in development Finish to Start - Common way how 2 tasks are linked
10 Simple GANTT Chart Critical path
11 GANTT Chart
12 Project Management Software Gantt Charts MS Project OmniPlan (Mac) ProPlanning (Mac) MS Excel et al. Calendar or event schedulers (many)
13 Data Management
14 Record Keeping Notebooks Electronic Paper Paper towel Journaling - The Lab Diary Protocols US Patents - first to invent Cosigning of lab notebooks critical for establishing invention ownership
15 Electronic v. paper Notebooks Electronic Initial software purchase Easy to search Can be shared remotely Resolves issues of poor handwriting Not all allow digital signing for patents Implementation and cost can be issue depending on the notebook Paper Easy to use, but hard to search (requires TOC) Patent ready Scanned backups necessary in case of theft or damage Cost can be an issue depending on the notebook and number of projects
16 Lab notebook guidelines Use a permanently bound book and ink Use a table of contents Enter all observations and data directly into the notebook. Prettiness is not important. Each experiment should stand on its own Explain nonstandard abbreviations Periodically scan notebooks in case of loss or damage Cross through blank pages and large spaces
17 Notebook signing U.S. patent assignment - First to invent (FTI) ROW - First to file Notebook witnessing Industry - all pages signed and witnessed Academia - learn what to sign Find out what works best for your lab
18 Patent dispute settlements Monsanto v. UC - UC awarded $100 million Bovine Somatotropin Genentech v. UC - UC awarded $200 million Human Growth Hormone Many Others Inventorship timing based on when your notebook was cosigned not when you signed it!
19 Anatomy of a Good Lab Notebook Title for TOC Projects kept in separate notebooks Link to pages Verified (cosign) Person not on same project Recorded by and date (FTI)
20 ELN software Dedicated ELN software Kalabie SmartTea Contur ACS NeuroSys Note taking programs MS OneNote MS Word/Excel NoteTaker/NoteShare
21 NoteTaker/NoteShare Software
22 Information Management Track collaborators, samples, chemicals, etc. Excel Spreadsheet Databases Filemaker Pro (Mac&PC) Access (PC only) Alpha Five (PC only) Paradox (PC only) Find out what works for you (benefit per time & effort)
23 Relational Databases Collection of related tables Queries (searches) used to combine data from different tables Large tables (Excel has limits) Customizable forms for data entry Calculations Retail databases can be used for LIMS Only as good as the information in them Be persistent Make data entry part of lab culture
24 Database - Forms with Flair
25 Database - Forms with Flair
26 Database - Collection of related spreadsheets Use Database Queries to gather information from different tables
27 A Simple Database
28 Number Crunching Use Excel to make templates for analyzing the same type of experiment Protein assays ELISAs Use Prism (GraphPad) or SigmaPlot if you have sophisticated kinetics or other data patterns that don t fit a linear regression Binding curves Kinetics
29
30 Making templates for repetitive tasks Use paste link function to copy data from 1 sheet to another Pasted data can be manipulated using graphs, formulas, etc. New data can be pasted without recreating graphs or formulas
31 Making templates for repetitive tasks
32 Using Paste Link Reorganize data for calculations or graphs Subsequent data can be formatted without having to create a new graph
33 Acknowledgment Ray Mernaugh, Ph.D. Vanderbilt Institute of Chemical Biology
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