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2022
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- July
2022
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2022
- Sunday
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- september
2022
- Sunday
- Monday
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- October
2022
- Sunday
- Monday
- Tuesday
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- Friday
- Saturday
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2022.06.23
IDT gblock resuspend
A, B, C, D, E, F
Taq PCR
A, B, C, D, E, F
Gel electrophoresis
A, B, C, D, E, F
2022.06.29
Transformation
pSB1A3 in DH5α
2022.06.30
Colony PCR
Pick four strains of bacteria from plate: 1, 2, 3, 4
Gel electrophoresis
1, 2, 3, 4
2022.07.01
Culturing
Pick two from each area: 1-1, 1-2, 2-1, 2-2, 3-1, 3-2, 4-1, 4-2
2022.07.02
Plasmid purification
1-1, 1-2, 2-1, 2-2, 3-1, 3-2, 4-1, 4-2
2022.07.04
Phusion PCR & Gel extraction
A, B
Digestion
A, B
Gel extraction
A, B
Ligation
A, B
2022.07.05
Phusion PCR & Gel extraction
E, F
Digestion
E, F
Gel extraction
E, F
Ligation
E, F
Transformation
A, B
2022.07.06
Phusion PCR & Gel extraction
C, D
Digestion
C, D
Gel extraction
C, D
Ligation
E, F
Transformation
E, F
Colony PCR & Gel electrophoresis
Pick eight plants from each plate A & B
A: three from each II, III, V area (A-2, A-3, A-5)
B: three from each IV, VIII (B-4, B-8)
2022.07.07
Transformation
E, F
Colony PCR & Gel electrophoresis
E => Pick three plants from plate
Ligation
E, F
Transformation
C, D
Culturing
A, B: Three tubes from each: A-2, A-3, A-5, B-4, B-8 (15 tubes in total)
2022.07.08
- A: His Ubx
- B: His EGFP Ubx
- C: PaPilA Ubx
- D: PaPilA 1-61 Ubx
- E: His Y4 mRFP Y293Y296
- F: His Y167 mRFP Y240
Colony PCR
E, F => Pick eight plants from each plate
E: E-1,E-2, E-3,E-4,E-5,E-6,E-7, E-8
F: F-1, F-2, F-3,F-4,F-5,F-6,F-7., F-8
Gel electrophoresis
Eight plants from E, F plate
Plasmid purification
Three tubes from each: A-2, A-3, A-5, B-4, B-8
Ligation
C
2022.07.18
Transformation
C, D, E, F
2022.07.19
Colony PCR & Gel electrophoresis
Pick eight plates from each plate: C, D, E, F
C: C-1, C-2,C-3,C-4,C-5,C-6,C-7, C-8
D: D-1, D-2, D-3, D-4, D-5, D-6, D-7, D-8
E: E-1, E-2, E-3, E-4, E-5, E-6, E-7, E-8
F: F-1, F-2, F-3, F-4, F-5, F-6, F-7, F-8
Culturing
Choose two tubes from each: C-2, C-3, C-7, C-8
Transformation
pSB3K3 in DH5α
Colony PCR & Gel electrophoresis
Pick eight plates from each plate: C, D, E, F
C: C-1, C-2,C-3,C-4,C-5,C-6,C-7, C-8
D: D-1, D-2, D-3, D-4, D-5, D-6, D-7, D-8
E: E-1, E-2, E-3, E-4, E-5, E-6, E-7, E-8
F: F-1, F-2, F-3, F-4, F-5, F-6, F-7, F-8
2022.07.20
Colony PCR & Gel electrophoresis
pSB3K3 in DH5α
Plasmid purification
two tubes from each: C-2, C-3, C-7, C-8
Digest check
C-2, C-3, C-7, C-8
Gel electrophoresis
Wrong result from digest check, so we use:
7/6 Digestion products
7/6 7/8 Ligation products
Culturing
4 mL from each: pSB3K3 B, C, D
Two tubes of 3 mL from each:
pSB1A3 C-11, C-14, D-11, D-12, D-15, E-10, E-14, F-9, F-10, F-11, F-13, F-16
2022.07.21
Plasmid purification
C-11, C-14, D-11, D-12, D-15, E-10, E-14, F-9, F-10, F-11, F-13, F-16
pSB3K3-1, pSB3K3-2
Digest check
C-11, C-14, D-11, D-12, D-15, E-10, E-14, F-9, F-10, F-11, F-13, F-16
Digestion & Gel extraction
A-2, B-8, pSB3K3-1
Transformation
pSB3K3 in DH5α
2022.07.22
Transformation
pSB1A3 A-2, B-8, C-14, D-11, E-14, F-11
Colony PCR
pSB3K3 1~8, C-17, C-18, C-19, C-20
2022.07.23
Culturing
pSB3K3 1~8, C-17, C-18, C-19
Plasmid purification
pSB3K3 1~8, C-17, C-18, C-19
Digestion & Gel extraction
Backbone: pSB3K3 1
Insert: C-14, D-11, E-14, F-11
Culturing
Take eight plants from pSB1A3
(C-14-1, C-14-2, D-11-1, D-11-2, E-14-1, E-14-2, F-11-1, F-11-2)
2022.07.24
Colony PCR
Take eight from each:
A-2, B-8, C-14, D-11, E-14, F-11 (pSB1A3 BL21)
Plasmid purification
C-14, D-11, E-14, F-11 (pSB1A3)
Digestion & Gel extraction
Backbone: pSB3K3 6
Insert: C-14, D-11, E-14, F-11
Buffer W2 Testing
Plasmid culturing
pSB1A3 BL21 A-2-2, A-2-5, B-8-2, B-8-5, C-14-7, C-14-8, D-11-1, D-11-8, E-14-1, E-14-7, F-11-3, F-11-7
2022.07.25
Digestion & Gel extraction
pSB3K3-1, pSB3K3-2, C-14, D-14, E-14, F-11
Digest check
C-17, C-18, C-19 (DH5α)
A-2-2, A-2-5, B-8-2, B-8-5, C-14-7, C-14-8, D-11-1, D-11-8, E-14-1, E-14-7, F-11-3, F-11-7 (BL21)
Ligation
A-2, B-8 (pSB3K3)
2022.07.26
Transformation
A-2, B-8 (pSB3K3 in BL21)
IDT gblock resuspend
G: LL37 Ubx mRFP
Taq PCR & Gel electrophoresis
G
Phusion PCR & Gel extraction
G
2022.07.27
Colony PCR
A-2, B-8, C-14, D-11, E-14, F-11 (pSB1A3)
Phusion PCR & Gel extraction
G
Digestion
G
Ligation
G in pSB1A3
2022.07.28
Transformation
pSB1A3 in BL21
Plasmid purification
A-2-9, A-2-10
Colony PCR
Three from each: A-2, B-8, C-14, D-11, E-14, F-11 (pSB1A3)
Ligation
For start unit: pSB1A3-1, A-2-9-1, A-2-9-2 (Label: E1-C, E1-A-2-1, E1-A-2-2)
2022.07.29
Expression
E1-C, E1-A-2-1, E1-A-2-2
Digest check
E1-A-2-1, E1-A-2-2
Transformation
pSB1A3 in DH5α
Plasmid purification
E1-A-2-1, E1-A-2-2
2022.07.30
Colony PCR
G (pSB1A3 DH5α)
2022.08.01
PCR for primer check
B: His EGFP Ubx
Wash bacterial cells
Bacteria collected every hour from E1-A-2-1, E1-A-2-2
Ligation
C(pSB1A3)
2022.08.02
Transformation
C, G (pSB1A3 in DH5α)
Sonicate
Bacteria collected every hour from E1-A-2-1, E1-A-2-2
Colony PCR
C-1, C-2, C-3 (pSB1A3-1 BL21)
For start unit: pSB1A3-1-1, D-11-9-5, D-11-9-6, F-11-10-4, F-11-10-5 (Label: E2-C, E2-D-1, E2-D-2, E2-F-1, E2-F-2)
2022.08.03
Expression
E2-C, E2-D-1, E2-D-2, E2-F-1, E2-F-2
Plasmid purification
E2-D-1, E2-D-2, E2-F-1, E2-F-2
Colony PCR
Four plants from each C, G (pSB1A3 DH5α)
For start unit: D
Four plants from each B, E
Digest check
E2-D-1, E2-D-2, E2-F-1, E2-F-2
2022.08.04
Plasmid purification
C-2, C-4, G-3
Colony PCR
C-1, C-2, C-3 (pSB1A3 BL21)
Digest check
C-2, C-4, G-3
2022.08.05
Digest check
C-2, C-4, G-3
2022.08.08
Phusion PCR & Gel extraction
C, G
Digestion
C, G
Ligation
C, G
2022.08.09
Transformation
C, G (pSB1A3 in DH5α)
pSB3K3 in BL21
2022.08.10
Digestion & Gel extraction
pSB1A3
Ligation
C, G (pSB1A3)
2022.08.11
Transformation
C, G in DH5α
Plasmid purification
C-1, C-2, C-3, C-4
Digest check
C-1, C-2, C-3, C-4
SDS-PAGE (Protein volume)
The 2, 4, 6, 8, 10, 12, 14, 16 hr from each: E2-D-1, E2-D-2, E2-F-1, E2-F-2
2022.08.12
Colony PCR
Eight plants from C (8/9 product)
Four plants from each C, G (8/11 product)
Colony PCR [Bioart]
BFP, YFP, GFP, RFP (pSB1C3 in DH5α)
2022.08.13
Plasmid purification
C-4, C-7, G-1, G-2, G-3
Digesst check
C-4, C-7, G-1, G-2, G-3
Colony PCR [Bioart]
Two from GFP: G-5, G-6
Six from BFP, YFP, RFP: B-5~10, Y-5~10, R-5~10
2022.08.14
Digest check
G-1, G-2, G-3
2022.08.15
Colony PCR
8/9 C: 15, 16, 17, 18, 19, 20
8/11 C: 5, 6, 7, 8, 9, 10
8/11 G: 5, 6, 7, 8, 9, 10, 11, 12
2022.08.16
Transformation
A, B in BL21
2022.08.17
SDS-PAGE (Protein concentration)
Expression 2
Colony PCR
A, B
2022.08.18
Expression
E3-C, E3-A-3, E3-A-4, E3-B-3, E3-B-4
Plasmid purification
E3-A-3, E3-A-4, E3-B-3, E3-B-4
Digest check
E3-A-3, E3-A-4, E3-B-3, E3-B-4
2022.08.19
Ligation
Backbone: pSB1A3
Insert: G
Digest check & Gel extraction
C-6, C-16
2022.08.24
Phusion PCR & Gel extraction
G
Colony PCR
pSB1A3 (Control)
For start unit: pSB1A3, A, B
Transformation
A, B in BL21
Digestion
G
Ligation
G
2022.08.25
Expression
E4-C, E4-A-3, E4-A-4, E4-B-3, E4-B-4
Digest check
E4-A-3, E4-A-4, E4-B-3, E4-B-4
Colony PCR
G
2022.08.26
Plasmid purification
G
Wash bacteria cells
E4
Sonicate
2, 4, 6, 8, 10, 12, 14, 16 hr of E4
2022.08.27
Digest check
G
2022.08.28
Sonicate
1, 3, 5, 7, 9, 11, 13, 15 hr of E4
SDS-PAGE
Expression 4
2022.08.31
Transformation
DH5α: pSB3K3, A, B
BL21: pSB3K3, A, B
2022.09.01
Colony PCR
pSB3K3, A, B (BL21)
pSB3K3, A, B (BL21)
pSB3K3, A, B (DH5α)
Transformation
pET-30a in DH5α
Expression
E5-Control, E5-A (pSB3K3)
2022.09.02
Colony PCR
pET-30a (DH5α)
Plasmid purification
E5-Control-2, E5-Control-3, E5-A-4
A-4, A-8, B-4, B-5
pET-30a-1, pET-30a-2
2022.09.05
Digest check
E5-A-4, A-4, A-8, B-4, B-5
Digestion
pET-30a-1, pET-30a-2
2022.09.06
Gel extraction
pET-30a-1, pET-30a-2
Ligation
C, D, E, F (pSB3K3)
Taq PCR
A, B, C, D, E, F, G
2022.09.07
Transformation
C, D, E, F (pSB3K3, DH5α)
D, F (pSB3K3, BL21)
Phusion PCR & Gel extraction
A, B, C, D, E, F, G
Digestion
A, B, C, D, E, F, G (pET-30a)
Colony PCR
Control, D, F (pSB3K3, BL21)
2022.09.08
Colony PCR
C, D, E, F (pSB3K3, DH5α)
Expression 6
E6-Control, E6-F-2, E6-F-3
Digestion & Gel extraction
pET-30a-3, pET-30a-4
Plasmid purification
E6-F-2, E6-F-3
Digest check
E6-F-2, E6-F-3
Transformation
N, O, P
2022.09.09
Ligation
A, F, G (pET-30a)
Digestion
pET-30abackbone
Wash bacterial cells & Sonicate
Expression 6
2022.09.11
Transformation
A, F, G (pET-30a, DH5α)
pSB3K3, BL21 plasmid
2022.09.12
Phusion PCR & Gel extraction
pET-30a
pSB3K3
Colony PCR
O, P
Transformation
N, P
Colony PCR electrophoresis check
N, P
2022.09.13
Colony PCR electrophoresis check
P
Transformation
I, J, Q, K, G
2022.09.14
Digest check
C-2, D-2, E-3, F-2 (pSB3K3)
Gel extraction
pET-30a
Colony PCR
D, E (pSB3K3, DH5α)
Ligation
A, B, C, D, E, F, G (pET-30a)
Transformation
L, J, I
2022.09.15
Colony PCR
L, J, I
2022.09.16
Plasmid Extraction
O
2022.09.17
Colony PCR
A, C, D, E, F, G (pET-30a), L
Expression 7
E7-Control, E7-F-3, E7-F-4 (pSB1A3, BL21)
2022.09.18
Expression 8
E8-Control, E8-F-3, E8-F-4 (pSB1A3, BL21)
Digest check
E8-F-3, E8-F-4
Transformation
O
Plasmid Extraction
L
Colony PCR
O
2022.09.19
Digest check
A-3, C-1, C-3, E-2, E-5, F-4, G-2 (pET-30a, DH5α), L
Transformation
pSB3K3 in BL21
2022.09.20
Expression 9
E9-Control, E9-F-3, E9-F-4 (pSB1A3)
Colony PCR
O
2022.09.21
Dialysis
E9-Control, E9-F-3, E9-F-4
Digest check
A-9, A-16 (pET-30a, DH5α), O
Plasmid Extraction
O, R
2022.09.22
Digest check
A-9, A-16 (pET-30a, DH5α), O, R
2022.09.23
Colony PCR
pSB3K3
Expression 10
E10-Control-1a3, E10-Control-3k3, E10-F
Digest check
O
2022.09.24
Transformation
A pSB1A3 to BL21
A pSB3K3 to BL21
Functional test 1&2
F
Colony PCR
pSB1A3 BL21
A
Transformation
R, L
2022.09.25
Expression 11
E11-Control, E11-A
Digestion
pSB3K3
Phusion PCR
G
2022.09.26
Plasmid purification
A
Digest check
A
Transformation
A, G
2022.09.27
Digest check
A
Functional test 3
Control, F
Colony PCR
Control-pSB1A3, Control-pSB3K3, F, G
2022.09.28
Expression 12
E12-Control-1a3, E12-Control-3k3, E12-F
Functional test 4
F
Colony PCR
R, L
2022.09.29
Bacteria Culturing
R, L
Plasmid Extraction
R, L
Digesst Check
R, L
Expression
R, L
2022.09.30
Colony PCR
E, G
Expression 13
Control-3k3, F
Expression 14
Control-1a3, Control-3k3, E
BioArt Protein Mixing
2022.10.01
Digest check
E
2022.10.02
Colony PCR
pSB3K3, F
2022.10.03
Expression 15
Control-3k3, F
2022.10.04
Expression 16
Control-3k3, F
2022.10.08
Expression 17
Control-3k3, F
A: His Ubx
B: His EGFP Ubx
C: PaPilA Ubx
D: PaPilA 1-61 Ubx
E: His Y4 mRFP Y293Y296
F: His Y167 mRFP Y240
G: K592100 (2022 kit, plate 1, well 17O)
H: K592024 (2021 kit, plate 1, well 17C)
I: E1010 (2021 kit, plate 3, well 12M)
J: I13500 (2021 kit, plate 6, well 21E)
K: I13500 (2021 kit, plate 2, well 16P)
L: J04450 (2021 kit, plate 6, well 4C)
M: K1033900 (2021 kit, plate 6, well 5N)
N: E1010 (2019 kit, plate 6, well 12M)
O: B0034 (2019 kit, plate 6, well 1M)
P: I13500 (2019 kit, plate 2, well 16P)
Q: I13500 (2019 kit, plate 6, well 21E)
R: K741002 (2019 kit, plate 2, well 17M)
S: K1033900 (2019 kit, plate 6, well 5N)
05.09 - 05.15
Learn more about Ubx: We want to make elastic fibers that can conduct electricity, finding that the protein Ubx could meet our needs. So we have an in-depth understanding of this protein, including its own characteristics and what kind of protein it can fuse with.
Search for conductive proteins: We searched for many kinds of conductive fibers, and decided to use pilA with better conductivity to fuse with Ubx to meet our thought, which we confirmed the production conditions of pilA and optimized its sequence.
Find other applications: We want to expand the application in other directions and try to make our fibers have various functions, so our goal is to find more usable proteins.
05.16 - 05.22
Learn Ubx spinning method: We are looking for the spinning method of Ubx, and the most suitable temperature and conditions for its spinning.
A new application—antimicrobial peptides(AMPs): We want to connect AMPs(antimicrobial peptides) to aptamer and then combine them with Ubx to make fibers with the ability of killing specific bacteria. However, the necessity of using aptamers is questionable, coupled with its difficult design. Therefore ,we decided to use only antimicrobial peptides for binding to Ubx.
05.23 - 05.29
Screening suitable AMP candidates: We searched for various AMPs and compared their differences to find out candidates fitting our needs.
Find the proteins and conditions that help wound healing: We want to start with wound dressings ,checking the ingredients of wound dressings currently on the market to know the conditions that aid wound healing.Beside,we attempt to improve the disadvantages of currently marketed wound dressings by adding these proteins to our fibers.
05.30 - 06.05
Find other applications: Moving on to other applications, we not only checked the scaffolding conditions for cell growth during tissue engineering, but found chelates that can bind to heavy metals, hoping to be used for water filtration and other purposes.
Meeting with Professor Ming-Chia, Li: We have had a discussion with Professor Ming Chia Li, who specializes in biomaterials. The professor gave us many suggestions and new ideas. Furthermore, We also exchanged knowledge about materials, and the professor allowed us to go into his lab for tensile testing of materials later.
06.06 - 06.12
Optimize the sequence of pilA and AMP
Plan the experimental process
Find other applications
06.13 - 06.19
Confirm appropriate conditions of candidate proteins in human body
Design the functional test of each protein and optimize the sequence
06.20 - 06.26
To know what affects protein conductivity
Design detailed experiment process and determine plasmid species
06.27 - 07.03
Follow-up experiment process design
07.04 - 07.10
Previous protein had problems with functional testing
Find another proteins that are easy to conduct functional test
07.11 - 07.17
New functional protein—lipase
07.18 - 07.24
Follow-up experiment process design
05.09 - 05.14
Learn MATLAB
05.16 - 05.22
Searching for softwares for protein structure prediction
05.23 - 05.29
Searching parameters for RFP expression
05.30 - 06.05
Simulation of how the Ubx protein and E.pili protein connect together through SWISS-MODEL
06.06 - 06.12
Learn MATLAB SimBiology
Expression Model I
- RFP biobrick
- derive formula
- find parameters
06.13 - 06.19
Expression Model II
- GFP biobrick
- derive formula
- find parameters
Expression Model III
- RFP + GFP biobrick
- derive formula
06.20 - 06.26
Sorting all data (parameters)
06.27 - 07.03
Learn Autodock, Materials Studio
07.04 - 07.10
Design verification experiment for expression models
Searching 3D printing models from previous teams
Meeting with professor Ming-Chia, Li
07.11 - 07.17
Protein structure prediction
- predict the structure of Ubx with AlphaFold
- label binding sites in fusion proteins with Pymol
07.18 - 07.24
Predict the structure of Ubx with I-TASSER
Derive formulas of hydrogel elasticity
Stress analysis with Autodesk Inventor
07.25 - 06.31
Meeting with professor Jhih-Wei, Chu
08.01 - 08.07
Model plan adjustments
- delete elasticity model
- maintain expression and protein structure model
Protein mixing model
- predict the fluorescence brightness over time
08.08 - 08.14
Expression model
- expression induced with different concentrations of IPTG vs the number of proteins
Protein mixing model
- wavelength turn to RGB formula
08.15 - 08.21
Protein structure prediction
- I-TASSER: confidence score checking
Binding region prediction (ANCHOR algorithm)
Protein mixing model
- design a Scaffold simulating model to change normal picture into fluorescence
08.22 - 08.28
Expression model: experimental verification design
- design biobrick
- design experiment steps
- checking protocol
02.29 - 09.04
Expression model: experimental verification design
Molecular dynamics simulation
09.05 - 09.11
Expression model: experimental verification
Protein structure prediction: AlphaFold2
09.12 - 09.18
Expression model: experimental verification
Protein mixing model
- convert wavelength to RGB
0919 - 09.25
Expression model: experimental verification
Binding region prediction: ANCHOR
- analyzing tyrosine binding ability
Protein mixing model
- scaffold model
09.26 - 10.02
Expression model: experimental verification
Binding region prediction: ANCHOR
Protein mixing model
- dealing with experimental data
- run the result of protein mixing model
10.03 - 10.09
Protein mixing model
- put the interactive result through time on WiKi
- design interactive result presentation
10.10 - 10.12
Tyrosine binding model
05.09 - 05.15
Establish future plans for HP events.
05.16 - 05.22
Write supporting document in Education Package
05.23 - 05.29
Make lecture slides in Education Package
05.30 - 06.05
6/02 Online meet-up with Professor Ming-Chia, Li
6/05 Online meet-up with team Jiangnan_China
Make board game in Education package (Script)
06.06 - 06.12
Make board game in Education package
06.13 - 06.19
Preparation for The 13th AFOB Regional Symposium (2022 ARS event)
06.20 - 06.26
6/26 Attend The 13th AFOB Regional Symposium (2022 ARS event)
06.27 - 07.03
6/29 Online meet-up with Professor Yu Yuan, Hsiao
7/03 Online meet-up with team Munich
07.04 - 07.10
7/04 Online meet-up with team CUG
7/05 Online meet-up with Huai En, Lu
7/09 Release “Synthetic Biology Classroom” video episode 1
07.11 - 07.17
7/12 Online meet-up with team HKUST
7/16 Release “Synthetic Biology Classroom” video episode 2
07.18 - 07.24
7/18 Online meet-up with team NCHU
7/23 Release “Synthetic Biology Classroom” video episode 3
07.25 - 07.31
7/26 Online meet-up with team KCL
7/30 Release “Synthetic Biology Classroom” video episode 4
08.01 - 08.07
8/02 Meet-up with GEMS_Taiwan
8/04 Second online meet-up with team KCL
8/06 7/12 Release “Synthetic Biology Classroom” video episode 5
8/05 Release workshop poster
Make RPG game in Education Package
08.08 - 08.14
8/13 Release “Synthetic Biology Classroom” video episode 6
8/14 Launch BioArt workshop #1
08.15 - 08.21
8/20 Release “Synthetic Biology Classroom” video episode 7
Make poster of Taiwan SynBio Conference
08.22 - 08.28
8/22,23 Attend Taiwan SynBio Conference
8/25 Launch BioArt speech
8/27 Release “Synthetic Biology Classroom” video episode 8
Make promotion video
08.29 - 09.04
8/31 Education event with Taipei First Girls High School
9/1 BioArt workshop with KCIS_Xiugang
9/3 Release “Synthetic Biology Classroom” video episode 9
Make promotion video
09.05 - 09.11
9/8 Education event with KCIS_Xiugang
09.12 - 09.18
9/15 NYCU_Formosa presentation
Workshop video editing
09.19 - 09.25
9/23 Entrepreneur visit in Hung Chou Fiber Industry
Workshop video editing
09.26 - 10.02
9/28 Bioart phase #3: artwork sharing
Design merchandise
10.03 - 10.09
10/9 Publish BioArt online exhibition
Design merchandise
10.10 - 10.12
BioArt online exhibition