22/05/2011 Object of this Course - - PDF document

22/05/2011 1

BioloMICS

• Additional logos

(if required) to go in this space The Atlas is funded by the Australian Government under the National Collaborative Research Infrastructure Strategy and further supported by the Super Science Initiative of the Education Investment Fund

Object of this Course

• Presentation Schedule

(Day 1 – Part 1)

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• 4. Search
• 5. History of changes
• 6. General options
• 7. Analysis Tools
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• Presentation Schedule

(Day 1 – Part 2)

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22/05/2011 2

• 1. Introduction –

What is BioloMICS?

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• 2. Registration and Login

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• More info: BioloMICS Software Help Manual, chapter 4 (p40)

BioloMICS Main Manager Window

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• 3. Records
• Duplicated names are not allowed
• Newly created records are appended at the end of the currently

displayed table

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More info: BioloMICS Software Help Manual, chapter 8 (p121-123)

• 3. Records
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More info: BioloMICS Software Help Manual, chapter 5 (p55)

• 3. Records
• Same value in selected records:
• Select the records
• Change value for wanted field in the tree
• Same value in selected fields:
• Select several text fields (Code E), and update one of

them

• Only when they have exactly the same properties!
• One can combine the update of several records and fields

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More info: BioloMICS Software Help Manual, chapter 8 (p123-124)

22/05/2011 3

• 3. Records
• Right-click on selected records:
• Show selected records
• Hide selected records
• These operations do not modify the data; they just apply to the

display

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More info: BioloMICS Software Help Manual, chapter 8 (p124)

• 3. Records
• By default all tables are sorted by ascending ID number
• There are two options to sort by:

Click on header of field

• Temporary
• One column/field can be sorted

Order by

• Permanently (sorting is kept within current layout)
• More columns/fields can be sorted
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More info: BioloMICS Software Help Manual, chapter 8 (p124-125)

• 4. Search
• There are two options to search by:

Simple Query

• Only one question at a time

Advanced Query

• It is possible to search by several questions or

conditions at the same time

• A query can be saved and reused later
• Exact match is the fastest way to search

More info: BioloMICS Software Help Manual, chapter 9 (p127-131)

• 5. History of Changes
• Every change made is recorded
• Click undo to return to the previous value

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• When batch changes are made, the undo action will also revert

all changes from a single batch action at once

More info: BioloMICS Software Help Manual, chapter 16 (p196-197)

• 6. General Options

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• 7. Analysis Tools
• Select records to

identify & reference records

• Set the characters to

be accounted for the identification

• You can change the

weighting, tolerance, & algorithm to be used.

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More info: BioloMICS Software Help Manual, chapter 11 (p136-140)

22/05/2011 4

• 7. Analysis Tools
• Nine different algorithms available (see manual for details)

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More info: BioloMICS Software Help Manual, chapter 12 (p141-156)

• 7. Analysis Tools

Seven step wizard instructions are given in each step: 1. Open picture 2. Define region of interest 3. Lane detection 4. Band detection 5. Set reference lane 6. Interpolation step 7. Results

• Export:
• Results to file
• Results to clipboard
• Profiles to BioloMICS

database

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More info: BioloMICS Software Help Manual, chapter 18 (p198-209)

• 7. Analysis Tools
• Used for managing samples

for DNA extraction and sequencing

• 13 movies available on

www.bio-aware.com Demos – LIMS

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More info: BioloMICS Software Help Manual, chapter 20 (p220-237)

• 7. Analysis Tools
• Double-click on F field to

view the pictures in the picture gallery

• Multiple picture viewer

show pictures from database and also from elsewhere

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More info: BioloMICS Software Help Manual, chapter 22 (p260-283)

• 7. Analysis Tools
• Double-click on picture in picture

gallery to start Object Detection and Measure on pictures

• Two options for Object Detection and

Measures on Pictures:

• Edge Detection
• Simple Measurement
• Export results to clipboard

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More info: BioloMICS Software Help Manual, chapter 22 (p260-283)

• 7. Analysis Tools
• Produce distribution maps based on latitude-longitude
• To retrieve the exact

positioning of locations around the world

• Correct spelling of places

in E field is important

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More info: BioloMICS Software Help Manual, chapter 23 (p284-291)

22/05/2011 5

• 8. Sequence Tools
• Standard sequence

formats can be loaded

• Experiment can be

saved and opened at any time

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More info: BioloMICS Software Help Manual, chapter 19 (p210-219)

• 8. Sequence Tools
• Align one sequence against another one
• Align a few sequences against Genbank and/or local
• Results will be stored in a folder name like: “MultiAlignRes10_14_2010_3_40_06_PM”

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More info: BioloMICS Software Help Manual, chapter 19 (p210-219)

• 9. Data Import
• Data can be imported in one or multiple tables at once
• Paste either tab-delimited data or fasta file format
• Choose:
• Append
• Merge Merge (- & + = variable) or Replace

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More info: BioloMICS Software Help Manual, chapter 13 (p157-175)

• 10. Data Export
• Many different options for

exporting data

• Export all or selected

records only

• Most options are shown in the movie, others are explained in

the manual

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More info: BioloMICS Software Help Manual, chapter 14 (p176-193)

• 11. Export to ALA and AMRiN
• Is part of your standard configuration
• Two modes:
• Automatic (scheduled job)
• Manual (run script to produce file, then upload at

http://www.ala.org.au/share/share-data/

• 12. Program Manager
• An own written function can be added to the software when wanted
• Two languages available:
• Visual Basic
• C#

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More info: BioloMICS Software Help Manual, chapter 21(p238-259)

22/05/2011 6

• 13. Background

BioloMICS Database Structure

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A table contains records with information in different fields

• 13. User Access

User A Profile in database Group X

Belongs to Each group has specific rights per table, field and per record

• 14. User’s Profile

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Warning!

Deletions cannot be reversed !

More info: BioloMICS Software Help Manual, chapter 5 (p48-51)

• 15. Groups

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More info: BioloMICS Software Help Manual, chapter 5 (p51-52)

16. Rights

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More info: BioloMICS Software Help Manual, chapter 5 (p52-54)

• 16. Rights - Example

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More info: BioloMICS Software Help Manual, chapter 5 (p52-54)

22/05/2011 7

• 17. Tables

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More info: BioloMICS Software Help Manual, chapter 5 (p55-59)

• 17. Tables

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More info: BioloMICS Software Help Manual, chapter 5 (p55-59)

• 17. Tables

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• All fields of the original table will be present in the new

table

• Equivalency between fields in each table will be

automatically established

More info: BioloMICS Software Help Manual, chapter 5 (p55-59)

• 17. Tables

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• Basic needed

fields will be created

• Possible to add
• r modify fields

that were created automatically

More info: BioloMICS Software Help Manual, chapter 5 (p55-59)

• 17. Tables

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• To modify a table: right-click on a table name, modify table
• To delete a table: right-click on a table name, delete table

A table containing fields cannot be removed!

Warning!

Deletions cannot be reversed !

More info: BioloMICS Software Help Manual, chapter 5 (p55-59)

• 18. Fields

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• To modify a field: right-click on a field name, modify field

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Deletions cannot be reversed !

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More info: BioloMICS Software Help Manual, chapter 5 (p59-64)

22/05/2011 8

• 18. Fields – Field Types
• Simple discrete, semi-discrete or continuous characters
• Maximum 1 state or value

For example: Temperature: 20.5

• A default, minimum and

maximum value can be given

• More info: BioloMICS Software Help Manual, chapter 6 (p67-69)
• 18. Fields – Field Types

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• Continuous range data

For example: (2) – 3 – 5 – (6)

• Minimum < = lower percentile < = higher percentile < = maximum
• Value must be numeric and positive

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p69-77)
• 18. Fields – Field Types

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D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• Fixed array of continuous data of type S
• Application To:
• 96 wells microplate continuous data
• 384 wells microplate continuous data
• Free array data, continuous

More info: BioloMICS Software Help Manual, chapter 5 (p77-79)

• 18. Fields – Field Types
• Maximum 15 simple discrete values

For example: “presence/absence” “yes/no/maybe” Result: Only one value can be true at the same time

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

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More info: BioloMICS Software Help Manual, chapter 6 (p79-82)

• 18. Fields – Field Types

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• Up to 5000 states

For example: colours, vegetation or climate Result: More than one value can be true at the same time

• D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

More info: BioloMICS Software Help Manual, chapter 6 (p82-85)

• 18. Fields – Field Types

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• Fixed array of discrete data
• Application To:
• 96 wells microplate continuous data
• 384 wells microplate continuous data
• Free array data, continuous
• +, -, weak, …

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p85-88)

22/05/2011 9

• 18. Fields – Field Types

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• Container for any file of any format (pictures, MS-Office documents,

trace files, etc)

• Maximum one file can be stored

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• Link to F field in another table containing a file
• Used to link more than one file to a record

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p88-93)
• 18. Fields – Field Types
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• Molecular Weights (MW) profile
• Storage: Vector of Real Numbers. Ex: 15; 20; 237; 500.
• Maximum one profile can be stored

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• Link to G field in another table containing MW
• Used to link more than one profile to a record

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

More info: BioloMICS Software Help Manual, chapter 6 (p93-96)

• 18. Fields – Field Types

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• Contains DNA or Protein Sequence
• Maximum one sequence can be stored

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• Link to N field in another table containing a sequence
• Used to link more than one sequence to a record

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p96-101)
• 18. Fields – Field Types
• Free text containing an unlimited amount of characters
• Keywords can be added to a dictionary to prevent typing mistakes

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

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More info: BioloMICS Software Help Manual, chapter 6 (p101-103)

• 18. Fields – Field Types

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• Link to records of another and associated table
• The other table = target table
• Link can also point to the same table
• For example: Link between strains (table 1) and species name

(table 2)

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p103-104)
• 18. Fields – Field Types
• List of hyperlinks pointing to websites
• Several hyperlinks can be added to one U field

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

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• More info: BioloMICS Software Help Manual, chapter 6 (p104-106)

22/05/2011 10

• 18. Fields – Field Types

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• Latitude & Longitude in degree/minute/second or in radian
• Altitude in Meters
• Precision Factor (PF) in Kilometers
• Maximum one location can be stored

Llink

• Link to L field in another table containing a location
• Used to link more than one location to a record

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p106-108)
• 18. Fields – Field Types

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• Free array of series of

continuous data

• Maximum one array

can be stored Wlink

• Link to W field in another table containing a list of paired values
• Used to link more than one list of paired values to a record

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

• More info: BioloMICS Software Help Manual, chapter 6 (p108-110)
• 18. Fields – Field Types
• Date with the following format: dd/mm/yyyy or mm/dd/yyyy
• Formats (US or European) can be set in the Options dialog

For example: 30-Mar-01 1:20:45 1937

• A calendar tool is also available

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

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• More info: BioloMICS Software Help Manual, chapter 6 (p110-112)
• 18. Fields – Field Types
• Simple discrete, semi-discrete or continuous characters
• The value must be an Integer

D, S, M, T, C, A, F, Flink, G, Glink, N, Nlink, E, Rlink, U, L, Llink, W, Wlink, H, I

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• More info: BioloMICS Software Help Manual, chapter 6 (p112-113)
• 19. Field Equivalency

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• Used when exporting a record from one table to another

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More info: BioloMICS Software Help Manual, chapter 6 (p113-114)

• 20. Layout
• To make tables and associated fields visible or not
• Without any associated layout, a previously created table or field

will remain invisible for the end user.

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• Check the layouts that should be visible

Warning!

Deletions cannot be reversed !!!!!!

More info: BioloMICS Software Help Manual, chapter 7 (p116-120)

22/05/2011 11

• 21. Database

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More info: BioloMICS Software Help Manual, chapter 5 (p43)

• 21. Database

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Warning!

Deletions cannot be reversed!

More info: BioloMICS Software Help Manual, chapter 5 (p44-45)

• 22. Web Version
• Publish data on your intranet
• Define which data will be available on the website
• Website is fully flexible

Define own pages Edit website menus Choose website colours etc

• Modify data in web configuration

changes direct visible at internet site

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More info: BioloMICS Software Help Manual, chapter 25 (p294-325)

• 22. Web Version - internet

Before publishing to internet:

• Think about http://amrin.org/ and http://www.ala.org.au/
• Is there a change that could be made to those sites?

For assistance setting up the website:

• Contact support@ala.org.au

Where to get support

These slides: http://www.ala.org.au/about/program-of-projects/biolomics/ BioloMICS support: http://www.bio-aware.com/ Atlas of Living Australia: http://www.ala.org.au/support/ support@ala.org.au Nathalie van de Wiele: nathalie@vdwiele.com

BioloMICS Software Help Manual Version 8.6.2.1

The Council of Heads of Australian Faunal Collections (CHAFC) The Council of Heads of Australian Entomological Collections (CHAEC) The Atlas is funded by the Australian Government under the National Collaborative Research Infrastructure Strategy and further supported by the Super Science Initiative of the Education Investment Fund Council of Heads of Australian Collections of Microorganisms (CHACM) The Council of Heads of Australasian Museum Directors (CAMD)

The Atlas of Living Australia Participants