Complementary Skills and Research Training Workshops

Complementary Skills and Research Training Workshops

The offered training is at the interface of mathematics, experimental biology and computer science. AccliPhot will integrate theoretical and experimental research from academia and industry and therefore put a strong emphasis on training scientists in complementary fields. The general approach of AccliPhot is to complement advanced and specialised hands-on training provided locally in the laboratories of the partners with network-wide training activities.

AccliPhot training activities

 

Training Event

Planned Date

Planned Venue

1

Complementary Skills Workshop 1

September 2013

Oxford, UK

2

Theory Workshop 1 + Metabolic Pathway Analysis Conference

September 2013

Oxford, UK

3

Lab Workshop 1

June 2014

Verona, Italy

4

Theory Workshop 2

September 2014

Düsseldorf, Germany

5

Complementary Skills Workshop 2

September 2014

Düsseldorf, Germany

6

Lab Workshop 2

May 2015

Halle, Germany

7

Complementary Skills Workshop 3

August 2015

Bantry, Ireland

8

Final Conference

 

April 2016

Saint Paul's Bay, Malta

 

Complementary skills workshop 1 - Management, impact and collaboration

Where: Corpus Christi College, Oxford, UK

When: 9-10th September 2013

Who: All ESR's

Aims: The Key aims of the workshop were to develop skills in the following areas:

  • cross-culture communication
  • collaboration especially within multidisciplinary research projects
  • project management
  • delivering impactful research

The workshop was delivered by Robin Henderson from MY Consultants. The handout is available here - Acciphlot_handout.pdf.

 

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Theory workshop 1 - Modelling Theory and Practice and Metabolic Pathway Analysis conference

Where: Corpus Christi College, Oxford, UK

When: 11-20th September 2013

Who: All ESR's and ER, associated group members

Aims: The workshop covered methods to analyse metabolic networks, with a focus on structural network analysis. Dynamic models will be covered in the second Theory workshop.

During the workshop the students were introduced to metabolic modelling and the concept of stoichiometry matrices as well as the null space and elementary modes. Elementary modes analysis was applied to real systems. This was followed by a brief introduction to the programming language Python and it was shown how a null space and elementary modes analysis can be performed with the Python language extension ScrumPy. The last two days were devoted to the analysis of genome-scale models. The process of building such models was discussed. Linear Programming and Flux Balance Analysis for the analysis of genome-scale models were introduced.

The lectures  and practicals were designed for researchers with little mathematical background.

The lecture slides can be found on the website of the Cell Systems Modelling Group (Oxford Brookes University).

In the second week the fellows attended the 2013 Metabolic Pathway Analysis Conference which deepened their knowledge about the structural (topological) analysis of metabolic networks, and in particular techniques allied to linear algebra, linear programming and computer modelling. A specialised Thermodynamics in Metabolism workshop was held to further their understanding of this important topic in metabolic network analysis. The conference provided our ESRs with great networking opportunities with other early career researchers as well as distinguished researchers in the field. The meeting format as a residential meeting strongly promoted the interactions between all participants.

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Lab workshop 1- Spectrometric Analysis of Photosynthetic Processes

Where: University of Verona, Verona, Italy

When: 8-12 June 2014

Who: All ESR's and ER, associated group members

Aims: In this 1-week workshop, ESRs and other personnel involved in AccliPhot have been introduced in biochemical and biophysical measurements, which are indispensable to characterise basic photosynthetic processes and to derive data for modelling. The format of the course was that of a case-study: WT and existing mutants of Cr (Photosystem (PS) I and II, cytochtome b6f- and stt7, the identity of which was not revealed until the end of the workshop) were experimentally analysed for their capacity to perform ST in small groups supervised by expert scientists. These proteins are required for state transitions, with different functions.

Day 1: Room temperature pulse amplitude modulated (PAM) and low-temperature (77K) fluorimetry to assess electron flow capacity and occurrence of state transitions.

Day 2: PSI, PSII and cytochrome b6f activity will be measured spectroscopically (single turnover flash and steady state redox kinetics).

Day 3: Biochemical assessment of photosynthetic complexes by thylakoid membrane purification, non denaturating gel or SDS-PAGE analysis and immunodetection of different complexes.

Day 4: Fractionation of membranes (from day 3) and measurements of absorption and fluorescence features of green bands cut from the non denaturating gels will be performed.

Day 5: Conclusion of the workshop with presentations of the results and a general discussion. The identity of the strains is revealed and a model for activation of state transitions in Cr is proposed.

To complement lab-work, every day a specialised lecture has introduce theoretical concepts of the applied techniques.

The LW1 was directly followed by the MTR meeting. This meeting was attended by all AccliPhot members (PIs, ESRs, ER), members of the scientific advisory board, the EU Project Officer and the external scientific reviewer. All AccliPhot ESRs presented their work and the AccliPhot booklet containing lay project descriptions written by the ESRs was distributed to all participants.

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Theory workshop 2 - Advanced Modelling Practice and Introduction to Programming

Where: Düsseldorf, Germany

When: 8-12 September 2014

Who: All ESR's and ER, external students

Aims: The second Theory workshop built on the skills obtained in TW1 and the previously introduced techniques of linear programming were employed to examine the genome scale models of Arabidopsis and Phaeodactylum. Further, the use of the modelling software to interrogate BioCyc databases was introduced as well as kinetic modelling and the most import points of the field of metabolic control analysis. Beside the lectures given by OE and MP, students had investigated a small kinetic model to learn how to use the modelling software to perform metabolic control analysis, and then moved on to the analysis of a previously published model of the Calvin Cycle.

The workshop has been attended by all AccliPhot fellows as well as a student of the ITN PHOTO.COMM and two external students of the HHU. Slides of the workshop can be found here

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Complementary skills workshop 2 - Writing and presenting

Where: Düsseldorf, Germany

When: 15-17 September 2014

Who: All ESR's and ER, external students

Aims: This workshop was taught by Mark Buchanan and Justin Mullins, two scientists with high experience in scientific writing and editing. During the 3-day workshop, writing skills for scientific papers and grant proposals had been improved. One key element of the workshop was an abstract writing exercise that the students had to complete and send in advance of the course. These texts were discussed with the experts in a one-to-one session during the workshop. Further, presentation skills were practised by the students who presented a piece of science in a lay way. This talk had been assessed by the other students and experts who gave valuable tips to improve their skills.

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Lab Workshop 2 - Proteomics and Mass-spectrometry workshop

Where: Martin Luther University, Halle-Wittenberg, Germany

When: 4-8 May 2015

Who: All ESR's and ER, associated group members

Aims: This 1-week workshop is organised in three modules. In module 1, the participants will learn how mass spectrometers work. By hands-on time on an LTQ Ion-Trap, they will develop a sense for data acquisition, starting with instrument tuning and calibration. Large-scale analysis of doubly charged peptide ions and protein and peptide quantification, including stable isotope labelling techniques such as iTRAQ, will be covered. In module 2, modifications necessary for analysing posttranslational modifications will be discussed, where, in the framework of AccliPhot, an emphasis will be placed on phosphorylation. Module 3 is concerned with data analysis and interpretation. Participants will be sensitised to the risk of false positive peptide identifications.

False discovery rates will be calculated to establish a general quality control framework. As an important contribution to this workshop, our associated partner 1, Dirk Walther, will teach bioinformatic analyses methods. All modules are paralleled by literature seminars. Through this workshop, the participants will be prepared to acquire proteomics data, develop experimental designs, acquire a general sense for data quality in high-throughput technologies and critically assess current systems biology literature.

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Complementary skills workshop 3 - Industry relevant skills

Where: Bantry, Ireland

When: 24-27 August 2015

Who: All ESR's and ER

Aims: This 4-days workshop will provide industry-relevant skills which will promote entrepreneurial initiatives by enabling the participants to develop commercialisation strategies of their research results. A whole day will be devoted to discuss ethical issues involved in the use of genetically engineered organisms, preparing the participants to actively communicate potentials and dangers to the general public.

Day 1 Morning: Intellectual properties issues in biotechnology, afternoon: technology licensing

Day 2: Ethical issues

Day 3: Environmental and economic risk assessment

Day 4: Business plan development

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Final Conference

Where: Malta

When: 26-29 April 2016

Who: open to all

Aims: This 4-day conference will bring together the world-leading experimental and theoretical scientists in the field of photosynthesis and present a platform in which the research results of the consortium as a whole will be disseminated. The ESRs are actively involved in conference organisation, further developing their organisational skills. Ample time for round-table discussions and networking activities will be allowed and a particular focus will be placed on the development of follow-up research projects. One evening is specially devoted to engage the general public, by holding a public evening lecture with following panel discussion. The organising committee will invite top-class scientists in the fields of photosynthetic research and systems biology as keynote speakers.

AccliPhot and the topic-related MC-ITN PHOTO.COMM have decided to organise a common final conference to attract even more scientist and interested laymen.

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