Jónína Gudmundsdottir (PhD student at the University of Tromsø) reports from a course on “Analysing Microbial Genomic Data” at the University of Birmingham
March 2020 . Author: Jónína Gudmundsdottir.
My PhD is in microbiology and my project aims to investigate if cytotoxic drugs used in cancer chemotherapy have a role in the evolution of antimicrobial resistance. As whole genome sequencing (WGS) of bacterial strains has become a standard procedure in most research laboratories, the expectations have simultaneously increased towards laboratory scientists to be able to not only generate their own data but to be able to analyse it as well. This is something I have felt strongly myself for a couple of years now, as I have been expected to include WGS data in my research, without having the bioinformatic skills required to analyse such data myself. Something that has resulted in me becoming completely dependent on the abilities of co-workers and collaborators to analyse such data on my behalf.
For those reasons I was thrilled to have the chance to attend a 5-day course in analysing microbial genomic data at the Institute of Microbiology and Infection at The University of Birmingham. The course, which took place from the 24th – 28th of February, was taught by world-leading scientists in the field of bacterial genomics and designed to give the knowledge and tools to perform high-level analysis of microbial genomic data sets to people with no background in bioinformatics.
The course was organised as a workshop, where everyone worked on their own personal computers, and we started with learning how to use ubuntu operating systems and to competently code in the command line as well as getting an introduction to the field of bacterial genomics. When everyone had been taught to code, the course moved over to an intensive week of genomics analysis. We were taught how to access sequencing files and how to check the quality of those before starting any further work. We performed assemblies and annotations as well as mapping and doing SNP calling on data from multiple strains before using the obtained data to do further downstream work including comparative genomics, phylogenetics and pangenome analysis. Every single day the course organisers included tips and tricks on how to better perform tasks using bash commands, allowing us to become more secure in our own coding abilities. The course was then broken up throughout the week with research talks, giving us an insight into how those skills can be translated into research projects.
Overall, I could not be happier about the course, which exceeded all of my expectations. Going to the UK I had some minimum coding skills but no experience or competence when it came to WGS analysis. That has in the span of a week changed dramatically, and I now feel confident enough to start working through my own genomic data without support.
I am very thankful to IBA for the travel grant, which made it possible for me to attend the course. It has not only given me skills necessary for the progress of my PhD but also helped me build my professional network and gain exposure to international researchers in the field.
Attendence of the 8th National Infection Biology/Microbiology Meeting (NDPIA) 14-15 October 2019
November 2019. Author: Christina Skår Saghaug
I had the pleasure of participating in the 8th National Infection Biology/Microbiology Meeting 14-15 October 2019 in Aronsborg, Sweden. I am currently a PhD student working on genetic variation metronidazole metabolizing enzymes in the parasite Giardia lamblia. The parasite infects up to 250 million humans every year, and is a contributor to diarrhea, and is therefore causing disease in low and middle income countries.
The meeting I attended was focusing on biology and microbiology in infections. These themes are relevant for my research field and I got the opportunity to extend my knowledge about certain methods within polymerase chain reactions, whole genome sequencing and genetic analyses that will come handy throughout my PhD. The participation was also an excellent opportunity to network with other professionals and experts within the infection and antimicrobial resistance research field. The meeting consisted of keynote sessions by experts, and oral and poster presentations by PhD students and PostDocs.
I was chosen to present my research as a poster with 3 minutes oral presentation. The title of my poster was: “Characterization of flavohemoprotein in Giardia isolates”. By being given this chance, I had the opportunity to receive feedback, train my presentation skills and discuss my research with other scientists. The participants were mainly Swedish, with some representatives from Denmark and Norway. Small Nordic conferences are great for networking, and I hope in the future, some projects can be developed between my research group in Bergen and other research groups in Sweden who work with the same pathogen or different pathogens, using methods we are interested in. In addition to participating at the meeting, I got to explore the small city of Aronsborg and the capital Stockholm.
I was so lucky to receive travel support from The National Graduate School in Infection Biology and Antimicrobials (IBA) to attend this meeting. I am very lucky and forever grateful to have had the possibility receive this support.
From the writing course “Better together” in Bergen, Norway
October 2019. Author Muhammad Assaduzzaman
Muhammad Asaduzzaman, PhD Research Fellow at the University of Oslo and IBA member, received funding from us to attend a course in Bergen. This is what he has written as a report from his course:
Since my arrival in Norway early this year, this is my first trip to any Norwegian city other than Oslo. When Tina informed the last minute offer to join a course on popular science writing in Bergen from 14-18 October, it seemed to be a great opportunity for me as a first year PhD student. This course was organized by DEEP (Norwegian Research School for Dynamics and Evolution of Earth and Planets) and the students came from three research schools – IBA (The National Graduate School in Infection Biology and Antimicrobials), NORBIS (National research school in bioinformatics, biostatistics and systems biology) and DEEP.
As mentioned in the course website, this is definitely a successful initiative to develop basic writing skill in clear and concise way. This course has redefined my way of thinking in writing both scientific and general context. We learn many things but forget again without practice. This 5 day course is a complete package of sharing idea, writing in own way, polishing with others’ feedback and development of a final draft. The basic, simple but important steps I have learnt here is the use of active voice, continued flow, cutting needless and repetitive words, use of strong voice and avoid the long noun/adjective strings. In addition, we have realized the beauty of peer review how it improves the write-up skill for self and others.
The most important instruments in a training course are the proactive mentor/instructor and attentive participants. Mathew Stiller-Reeve, senior Meteorological researcher, school teacher, science communication expert and founder of SciSnack writing community is such a wonderful person to conduct this type of courses. Maybe we were the great attendee as well ( ). Because Mathew evaluated us as “You all impressed me by your hard work and development throughout the course. I really enjoyed watching your articles develop throughout the week”
Disregarding the flow we learnt, I can’t resist myself to tell about the city of Bergen. Bergen is a nice green city with an amazing amalgamation of sea and hills. I booked my hotel (unintentionally) near the most of the tourist attractions like Mount Floyen and the Funicular (Floibanen), Bryggen, Fish Market, theatre hall, several museums in university of Bergen, Bergenhus fortress etc. I was fortunate to visit the Natural History Museum when it was reopened after 3 years’ restoration process on October 14. I really enjoyed my stay in this city of scenic beauty with little boring rain.
Finally, my impression about this basic writing course is that all PhD students in their first year should attend this interdisciplinary training. The organizers can also think of an advanced course on scientific article writing for those who have attended this course and some sort of grant writing training for final year PhD students and postdocs.
I express my gratitude to IBA for the travel support as well as for the opportunity to attend this excellent course.
Balint Csoboz is back from a workshop on “Epigenetics of infectious and non-communicable diseases” in Cape Town South Africa
September 2019. Author: Balint Csoboz.
Balint Csoboz, post doc at the University of Tromsø and IBA member, received funding from us to attend a course in South Africa. This is what he has to report from the stay:
Between the 16th and the 19th of September, I was attending the workshop “Epigenetics of infectious and non-communicable diseases” in Cape Town South Africa. The meeting was organized by the South African component of the ICGEB (International Center for Genetic Engineering and Biotechnology). I have received partial funding from the meeting organizers for the attendance and the reason I applied for the support of IBA was to complement this funding in order to be able to manage the travel costs for the course.
ICGEB is an intergovernmental organization funded by the United Nations, which runs 46 state-of-the-art laboratories and forms an interactive network with over 65 Member States. ICGEB also offers a set of courses (https://www.icgeb.org/activities/meeting-and-courses/) and opportunities for short and long-term PhD/postdoc fellowships (https://www.icgeb.org/activities/fellowship/) to which I would highly encourage anyone to check out and apply for.
The workshop was focusing on many interesting aspects of epigenetics associated with infectious diseases as the epigenetics of host-pathogen interactions, the manipulation of epigenetics as host-directed drug therapy for infectious and non-communicable diseases, the analysis of micro- and long non-coding micro RNA in different pathologies or the role of epigenetics in modulation of host immune responses in diseases. This workshop provided insights of methods and models to identify epigenetic targets such as DNA methylation, covalent modification of histones, and the expression of non-coding RNA. During the poster sessions, I was introduced to methods that will certainly benefit my research on virally induced cancer. Like the technique of performing dual RNA sequencing of the host and infectious agent during infection and the usage and design of artificial epigenetic (gene) silencing by the means of gene editing.
I also felt very lucky because I had the chance to get familiar with the history and the culture of the host country and visit the surroundings of Cape Town during the meeting. Especially, hiking the Table Mountain was a great experience, which is elected to be one of the Natural wonders of the world.
I feel that my attendance of the workshop was fruitful and rewarding. I managed to familiarize myself with the field of epigenetics and non-coding RNA research, which would be very useful for my postdoctoral project.
I am grateful for the support of IBA, which allowed me to participate in this course and have this fantastic experience.
PhD student Diana Karina Diaz Canova is back from a course on Viral Bioinformatics and Genomics
October 2019. Author : Diana Karina Diaz Canova.
Diana Karina Diaz Canova, PhD student at the University of Tromsø, recently received funding from IBA to attend a course on Viral Bioinformatics and Genomics in Scottland.
She just came back, and you can read under what she says about her research and the bioinformatic training course!
My PhD research project is focused on improving MVA-vectored vaccine safety by determining potential recombination between MVA-vectored vaccine and naturally occurring Fennoscandian cowpox viruses (CPXVs) during coinfection/superinfection of mammalian cells. The risk of recombination is considered low because MVA multiplies poorly in most mammalian cells. However, we have demonstrated recombination occurred between MVA vaccine vector and CPXV. As part of my PhD project, I will analyse the genomes of hybrid progeny viruses from recombination between MVA – vectored vaccine and Cowpox virus. These genomes were sequenced by Next Generation Sequencing technology. However, successful analysis of these genomes sequences requires a good knowledge of bioinformatics analyses.
Therefore, I was motivated to attend the 5th Annual Training Course on Viral Bioinformatics and Genomics (19-23rd Aug 2019) organised by the Medical Research Council (MRC) – University of Glasgow Centre for Virus Research (CVR). I believed that attending the course will equip me with the right bioinformatic tools and also the impetus to analyse my sequence data.
The course was focused in analysing high-throughput sequence (HTS) datasets using bioinformatics tools, UNIX command-line and bash scripts. During the five-day course, different topics such as HTS sequencing technologies, reference assembly, variant calling, de novo assembly, metagenomics analyses, phylogenetic analysis etc. were covered through lectures and practical sessions.
The course was well structured and organized in such a way making it easy to comprehend for participants, like me with basic experience of UNIX command lines. The course coordinators dedicated the first day to introduce the UNIX command lines. In addition, after every lecture we had a practical session where we could put what we have learnt into practice. During the practical sessions, we analysed viral genome sequences using different bioinformatics tools.
The instructors used fun and creative ways such as Lego building for teaching reference assembly. The courses instructors were not only bioinformaticians but have extensive knowledge and real hands on experience in viral genome sequence analysis. This was quite helpful because we could discuss the current challenges we are facing in our individual project with them. I have got some feedback which I intend incorporating into my subsequent analysis.
Attending the course was a good and rewarding experience. Although the five days course was intensive, it was at the same time very productive because I could learn the main bioinformatics tools that are relevant to achieve the goals of my PhD research project.
I would like to thank to the National Graduate School in Infection Biology and Antimicrobials (IBA) for grating me the travel grant assistance to attend this course.
PhD student Christopher Frölich is back from a course on Structural Bioinformatics
September 2019: Author: Christopher Frölich.
PhD student from the University of Tromsø, Christopher Frölich, received funding from IBA to attend a course on Structural Bioinformatics in the UK. He just came back, and you can read his report under.
From the 16th to the 20th of September 2019 I visited the Wellcome Genome Campus in Cambridge to attend a course on Structural Bioinformatics. The course was organised by the European Molecular Biology Laboratory (EMBL), was internally oriented, and explored the various usages of bioinformatic data for structure determination. The talks were given by several different speakers and were always broken up into two parts; the first being an in-depth lecture and the second being a series of hands-on exercises to apply what we had just learned. During the practical parts, we got the opportunity to explore situations such as how mutations may change or interfere with pre-existing enzymatic functions, as well as molecular docking.
My personal highlight was one of the molecular docking experiments where we modelled protein-protein interactions. In addition, each participant had the opportunity to present their own work in form of a poster, leading to fruitful discussions and networking sessions amongst us attendants.
I am quite happy that I was able to attend this course since it provided insights into how to use bioinformatic data to predict structures. In addition, the speakers provided helpful open access tools to solve different scientific questions.
The Wellcome Genome Campus is modern, offers everything you need for a short term stay, and is roughly 30 minutes from the city centre of beautiful Cambridge.
I really would like to thank IBA for providing the travel grant and making this fantastic experience possible.
PhD student Syeda Mariam Riaz is back from an EMBL course on “Finding evidence in research publications”
September 2019. Author: Syeda Mariam Riaz.
PhD student from the University of Bergen, Syeda Mariam Riaz , received funding from IBA to attend an EMBL-EBI course on “Finding Evidence in Research publications” at the Wellcome Genome Campus in Cambridge, UK. This is what she has to report on the stay.
My PhD study aims to understand the immune pathogenesis of primary and post-primary tuberculosis using human material from the pre-antibiotic era. Primary and post-primary tuberculosis are two different disease entities caused by Mycobacterium tuberculosis. Experimental studies using various animal models have given useful insight into immune pathogenesis of primary TB, characterized by the granulomatous immune response which is very effective in controlling infection. However, there is a paucity of information on the immune pathogenesis of post-primary TB. Untreated human tissue was no more readily available after the introduction of antibiotics in the 1950s. This forced investigators to develop and use animal models for study. Use of animal models and lack of availability of human tissue for confirmation resulted in a new paradigm for TB pathogenesis dating back to the late 20th century. This has guided the research on TB since then and unfortunately diverted the focus from the true pathogenesis of post-primary TB.
My PhD thesis requires a lot of literature review of difficult to access articles of the early 19th Century. To increase my understanding of the literature review I went to Hinxton, UK to attend a two-day workshop on Finding Evidence in Research Publications arranged by EMBL. It was a very informative workshop where I was introduced to Europe PMC, an EMBL data resource site. In the workshop, they also taught us how the researcher shares and cite data. We were introduced to different tools to search for data cited in the literature along with methods of text mining and annotation and searching for datasets on a specific research topic. It was for the first time that EMBL was organizing such workshop and this provided us with great opportunity to learn. I also got the chance to meet researchers from diverse background, to discuss new ideas with them and learn from their experiences.
I am very grateful to IBA for sponsoring this course as it helped me build a network and gain international experience and exposure.