From developing software to building community in bioinformatics: How to find your niche in science.

Over the past decade, bio-computational research has advanced rapidly allowing large-scale characterization of genes, transcripts, and proteins, and resulting in a deluge of -omics data. Simultaneously, high-throughput bioinformatic approaches have been developed for the analysis of such data, identifying previously unknown molecules, their interactions, and their functions. I was first introduced to such techniques and the potential of bioinformatics in biological science during my masters at b-it in University of Bonn. This interest in the bio-computational tools, piqued during my masters and internship in Max Planck, inspired me to undertake a PhD at the University of Würzburg, leading me to my current position at EMBL Heidelberg. In my talk at the b-it lecture series, I will reflect on the last 8 years and share some of the lessons learned as a computational biologist while finding my niche in science as a community manager.

Transcript

1. Malvika Sharan Computational Biologist & Community Outreach Coordinator From Developing Software to Building Community in Bioinformatics: Finding Your Niche in Science.
2. 2 I’ll Talk About… • My research work as computational biologist • This won’t be your typical science talk. • Some challenges, efforts & lessons learned • Final thoughts & take home message
3. Bioinformatic Research Identification and Characterization of RNA-Binding Proteins in bacteria 3
4. RNA-Binding Proteins (RBPs) RBPs play regulatory roles in gene expression 2 CsrA-RNA complex (PDB: 2MFC) Bacterial RBPs can regulate virulence, motility etc. Hfq-RNA complex (PDB: 1KQ2) RBP functions are often linked to their domains Lunde et al., Nat. Rev.2007 Domain Binding site RNA 5’ 3’ Post-transcriptional control PubMed publication trend for RNA-binding 24 June 2018 4 4
5. Eukaryotic vs. Bacterial RBPs • Several studies for the proteome-wide identification of human RBPs • Using high-throughput sequencing and protein mass spectrometry methods Lack of such global screening studies in bacteria due to technical limitations 15 families, < 25 RBPs are known in bacterial species from various studies Gerstberger et al., Nat Rev. 2014 Van Assche et al., Front microbio. 2015 RBPs in eukaryotes: 1,111 families, 1,542 proteins 24 June 2018 5 5
6. Identification of Eukaryotic RBPs Functional annotation by homology mapping Human protein Homolog in mouse Experimentally identified RNA binding domain: RNA Recognition Motif (RRM) RRM domain Using a short functional motif as a query 24 June 2018 7 7
7. elegans Characterisation of Eukaryotic RBPs Multiple alignment to detect domain consensus RNA Recognition Motif 24 June 2018 9 9
8. Characterisation of Eukaryotic RBPs Domain containing RBPs Castello et al., Cell. 2012; Castello et al., Mol Cell. 2016 Multiple alignment to detect domain consensus RBD containing proteins Experimentally derived data constitute a resource for the method development in bioinformatics 5 RNA Recognition Motif K-Homology Cold Shock Domain DEAD Helicases 24 June 2018 10 10
9. Developed a Software Pipeline APRICOT Analysing Protein-RNA Interaction by Combined Output Techniques Uses eukaryotic domain information to identify, score and computationally annotate RBPs in query proteins/proteomes with sensitivity and specificity > 0.9. 24 June 2018 11 http://malvikasharan.github.io/APRICOT/ 11
10. Let’s step back… 12 https://unsplash.com/photos/xGkhQpBN9X8
11. Let’s step back… This wasn’t supposed to be a typical science talk! 13 https://unsplash.com/photos/xGkhQpBN9X8
12. My PhD in Nutshell 14 Worked with three groups during my PhD at Institute of Molecular Infection Biology, Uni. Würzburg: • Jörg Vogel (RNA biology) • Ana Eulalio (host-pathogen interaction) • Konrad Förstner (bioinformatic software)
13. My PhD in Nutshell 15 Worked with three groups during my PhD at Institute of Molecular Infection Biology, Uni. Würzburg: • Jörg Vogel (RNA biology) • Ana Eulalio (host-pathogen interaction) • Konrad Förstner (bioinformatic software) • Several collaborations, several projects, several scientific opportunities, great learning and networking environment
14. Applied My Work to Different Projects Analysis of 1,022 bacterial effector proteins Critical Assessment of Functional Annotation (CAFA) - 2, GO based function annotation of > 1 million bacterial proteins Functional characterization of protein families 16
15. 17 https://unsplash.com/photos/DoA2duXyzRM Path to Science Communication & Community Engagement
16. 18 • Through collaborations, I learned about and contributed to open science • Co-founded WUBSyB (Würzburg Unseminar in Bioinformatics and Systems Biology) to create platform for people to exchange bioinformatic skill in an informal setup • Represented Uni-Würzburg as a speaker of Doctoral Researchers Council for 3 years Science Communication & Community Engagement
17. 19 • Taught RNA-Seq analysis and data exploration to the biologists • Selected by Scifund Outreach Challenge to be trained at outreach skills • Joined Software Carpentry as a volunteer trainer to learn skills to teach programming 2015 2018 Science Communication & Community Engagement
18. 20 What Led Me Here? https://unsplash.com/photos/TamMbr4okv4
19. 21 Mentors, Peers & Aidan Budd - Community building, communication, Ally Konrad Förstner - Reproducibility, open access, PhD mentor Everyone who ever believed in me. Personal Network - Family, friends, community https://unsplash.com/photos/x1Qw2gCPMUU
20. My Path to Science Communication 22 • Identified my interests beyond research work • Open Science • Community building • Science communication • Actively participated in meetings and conferences • Learned about other career opportunities • Expanded network – kept myself involved • Co-authored papers with such collaborations
21. My Path to Science Communication 23 • Identified my interests beyond research work • Open Science • Community building • Science communication • Actively participated in meetings and conferences • Learned about other career opportunities • Expanded network – kept myself involved • Co-authored papers with such collaborations • Was invited to interview for my current job!
22. Computational Biologist at EMBL: What was in it for Me? 24 EMBL Bio-IT • Join a bioinformatic group as an outreach person to work on protein motif • Join Bio-IT bioinformatic project to provide opportunities for training and collaboration among scientist in EMBL • Provide outreach and training support beyond EMBL through the de.NBI project Toby Hodges (Bio-IT Project co-coordinator) Toby Gibson (EMBL Group Leader)
23. 25 Austria 1974 Denmark 1974 France 1974 Germany 1974 Israel 1974 Italy 1974 Netherlands 1974 Sweden 1974 Australia 2008 Argentina 2014 Switzerland 1974 United Kingdom 1974 Finland 1984 Greece 1984 Norway 1985 Spain 1986 Belgium 1990 Portugal 1998 Member States 24 Associate Member States Ireland 2003 Iceland 2005 Croatia 2006 Luxembourg 2007 Czech Republic 2014 Malta 2016 Hungary 2017 Slovakia 2018 Poland 2014 Lithuania 2015 Prospect Member States EMBL Member States
24. EMBL is a Flagship in Europe EMBL’s organisational structure serves as a model for other research institutions 26 Image copyright: EMBL
25. EMBL Sites 27 > 1600 people > 80 nationalities Hinxton Grenoble (ESRF) Structural Biology Hamburg (DESY) Structural Biology Heidelberg Life Sciences Rome Epigenetics & Neurobiology Bioinformatics Barcelona Tissue Biology & Disease Modeling Image copyright: EMBL
26. 28 Image by: Toby Hodges, EMBL Growing Interests in Bioinformatics
27. 29 Interdisciplinary & Collaborative Research at EMBL Image copyright: EMBL
28. 30 Bio-IT – Building Community & Training Capacity Image by: Toby Hodges, EMBL
29. 31 Supporting Bioinformatics Community: EMBL Bio-IT & Beyond Aidan Budd Image by: Toby Hodges, EMBL
30. 32 Supporting Bioinformatics Community: EMBL Bio-IT & Beyond Toby Hodges Image by: Toby Hodges, EMBL
31. • BMBF supported Cooperation of the German bioinformatics community with international bioinformatics network structures • 8 service centres focusing on the global Bioinformatics topics • Heidelberg Center for Human Bioinformatics (HD-HuB) • RNA Bioinformatics Center (RBC) • Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi) • Bioinformatics for Proteomics (BioInfra.Prot) • German Crop BioGreenformatics Network (GCBN) • Center for Biological Data (BioData) • Center for Integrative Bioinformatics (CIBI) • de.NBI Systems Biology Service Center (de.NBI-SysBio) International, National and Regional Support: de.NBI 24.06.18 33 33
32. Regional & Institutional Level Effort: HD-HuB Node 24.06.18 34 Unites bioinformatics expertise & computational resources of distinguished institutions 34
33. Regional & Institutional Level Effort: HD-HuB Node 24.06.18 35 Unites bioinformatics expertise & computational resources of distinguished institutions 35
34. Combining Resources: Collaborative Training Activities • Creating opportunities by combining the best resources from different communities • EMBL’s training capacity and infrastructure • de.NBI’s cloud compute and Europe-wide audience • Software and Data Carpentry courses • External trainers for specialized courses and future collaborations 36 As of June 13, Bio-IT has offered 50 courses 0 5 10 15 20 25 2012 2013 2014 2015 2016 2017 2018 Training activities: Bio-IT and de.NBI Bio-IT Collaboration de.NBI
35. 37 Supporting Bioinformatics Community: EMBL Bio-IT & Beyond Contributing to building other local communities • Hosting event series for local researchers Local Outreach Activities
36. 38 Supporting Bioinformatics Community: EMBL Bio-IT & Beyond Wider Outreach Activities Contributing to building other local communities • Hosting event series for local researchers Contributing to international communities: The Carpentries • Co-organized the 1st conference in Dublin Image: Berenice Batut Local Outreach Activities
37. 39 Supporting Bioinformatics Community: EMBL Bio-IT & Beyond Community Calls for Community Builders: Exchange Notes!
38. Challenges in Supporting Communities 40 Promote an inclusive culture & normalizing diversity and equality Making community efforts visible and attract volunteers Enhance capacity, knowledge transfer & collaborations
39. Lessons Learned: Things won’t always work, but when they do – they create a ripple effect! Promote communication, Encourage volunteering. Acknowledge their work. 41 Be open to a wider audience, Identify interests. Develop active groups. Be consistent persistent, when organizing *events. Engage Positively. Diversity must exist in the core of a community. Give everyone a fair chance.
40. Let’s step back a little more… 42 https://unsplash.com/photos/xGkhQpBN9X8
41. B-it Welcome Day: M.Sc Life Science Informatics Class 2010-2012 43
42. • I never programmed a single line of code until I arrived in Bonn • Failed my first programming test (it was Java!) • Didn’t think I was “Techie” enough to get it 44 How did my masters inspire me to pursue PhD? https://unsplash.com/photos/ukzHlkoz1IE
43. • I never programmed a single line of code until I arrived in Bonn • Failed my first programming test (it was Java!) • Didn’t think I was “Techie” enough to get it • All these happened in the first 4 months 45 How did my masters inspire me to pursue PhD? https://unsplash.com/photos/ukzHlkoz1IE
44. • I never programmed a single line of code until I arrived in Bonn • Failed my first programming test (it was Java!) • Didn’t think I was “Techie” enough to get it • All these happened in the first 4 months • But, then I got practical internships • B-it, Uni-Bonn – Data organization • Bayer – Perl project for gene expression • Max Planck of Aging (1.5 years) • Python project, thesis, 1st publication 46 How did my masters inspire me to pursue PhD? https://unsplash.com/photos/ukzHlkoz1IE
45. https://unsplash.com/photos/YVgOh8w1R4s After my masters I didn’t think I had mastered any particular subject and here is what I learned… 47
46. Doing a Masters Doesn’t Make you a Master of a Subject… 48 https://www.vit.edu.au/master-of-information-technology-systems-mits/
47. Doing a Masters Doesn’t Make you a Master of a Subject… 49 …and that’s a successful higher education https://www.vit.edu.au/master-of-information-technology-systems-mits/
48. Doing a Masters Doesn’t Make you a Master of a Subject… 50 …and that’s a successful higher education …because it left you more curious than you first started. https://www.vit.edu.au/master-of-information-technology-systems-mits/
49. Here are what I picked up in my masters 51 https://unsplash.com/photos/o2glCCYUCe8
50. Here are what I picked up in my masters • Overview of new topics: science, soft skills, career … 52 https://unsplash.com/photos/o2glCCYUCe8
51. Here are what I picked up in my masters • Overview of new topics: science, soft skills, career … • Opportunities to explore different tools 53 https://unsplash.com/photos/o2glCCYUCe8
52. Here are what I picked up in my masters • Overview of new topics: science, soft skills, career … • Opportunities to explore different tools • Study-work model: chances to have practical internships 54 https://unsplash.com/photos/o2glCCYUCe8
53. Here are what I picked up in my masters • Overview of new topics: science, soft skills, career … • Opportunities to explore different tools • Study-work model: chances to have practical internships • Soft introduction to the international culture 55 https://unsplash.com/photos/o2glCCYUCe8
54. Here are what I picked up in my masters • Overview of new topics: science, soft skills, career … • Opportunities to explore different tools • Study-work model: chances to have practical internships • Soft introduction to the international culture • Expanded my communication skills • Speaker of the LSI 2009-11 class • 1-on-1 training opportunities • International colleagues and friends 56 https://unsplash.com/photos/o2glCCYUCe8
55. Here are what I picked up in my masters • Overview of new topics: science, soft skills, career … • Opportunities to explore different tools • Study-work model: chances to have practical internships • Soft introduction to the international culture • Expanded my communication skills • Speaker of the LSI 2009-11 class • 1-on-1 training opportunities • International colleagues and friends • …and a score card that nobody looked at. 57 https://unsplash.com/photos/o2glCCYUCe8
56. How to Find Your Niche in Science! 58
59. I Asked Others How they Found Their Niche 61
60. Here are a few responses 62 https://unsplash.com/photos/GwsXX--WwjU
61. Find what annoys you: fix it in your own way! 63
62. Develop interests & skills: stay open to chances! 64
63. Build authentic relationships: use your privilege for good! 65
64. Don’t only try to find your niche: ‘Found’ your niche! 66
65. Niche is overrated! 67 https://unsplash.com/photos/xGtHjC_QNJM Identify topics that excite you be genuinely interested and ask all the WTF (What’s the fact?).
66. Niche is overrated! 68 https://unsplash.com/photos/xGtHjC_QNJM Stay Curious Not understanding something doesn’t mean you can’t learn it. Identify topics that excite you be genuinely interested and ask all the WTF (What’s the fact?).
67. Niche is overrated! 69 https://unsplash.com/photos/xGtHjC_QNJM Stay Curious Not understanding something doesn’t mean you can’t learn it. Explore ideas you come across but be a little sceptical. Identify topics that excite you be genuinely interested and ask all the WTF (What’s the fact?).
68. Niche is overrated! 70 https://unsplash.com/photos/xGtHjC_QNJM Stay Curious Not understanding something doesn’t mean you can’t learn it. Explore ideas you come across but be a little sceptical. Identify topics that excite you be genuinely interested and ask all the WTF (What’s the fact?). Learn to say yes but also learn to say no.
69. Niche is overrated! 71 https://unsplash.com/photos/xGtHjC_QNJM Learn to say yes but also learn to say no. Stay Curious Not understanding something doesn’t mean you can’t learn it. Explore ideas you come across but be a little sceptical. Identify topics that excite you be genuinely interested and ask all the WTF (What’s the fact?). Expand your network value your relationships
70. They were right when they said academia isn’t easy! 72 https://medium.economist.com/why-doing-a-phd-is-often-a-waste-of-time-349206f9addb
71. https://unsplash.com/photos/IR3hrNqyM90 73 Challenges as a PhD Student • Need of publications: in high impact factor journals • Insecurity of job/funding: standard academic rule • Over commitments à lack of work-life balance à burn-out • Lack of gender diversity: often undiscussed and unnoticed • Nobody talked about the importance of mental health
72. 74 https://unsplash.com/photos/5bYxXawHOQg Take Home Message
73. 1. Be different 75
74. 1. Be different 76 https://unsplash.com/photos/NL3cq2B33yw
75. 2. It’s not a competition 77 https://unsplash.com/photos/chuzevDl4qM
76. 2. It’s not a competition: share your knowledge! 78 https://unsplash.com/photos/chuzevDl4qM
77. 3. You are in it for a long run 79 https://unsplash.com/photos/vnpTRdmtQ30 https://unsplash.com/photos/vnpTRdmtQ30
78. 3. You are in it for a long run: have fun! 80 https://unsplash.com/photos/vnpTRdmtQ30
79. 4. You will fail 81 https://weheartit.com/entry/219963210
80. 4. You will fail: its not a failure! 82 https://weheartit.com/entry/219963210
81. https://unsplash.com/photos/pqHRNS8Mojc "The only way to do great work is to love what you do. If you haven't found it yet, keep looking. Don't settle." — Steve Jobs 83
82. Acknowledgements The Carpentries (Software & Data Carpentry) Community All past and present mentors, trainers, & contributors of Bio-IT 84 EMBL Bio-IT Toby Hodges (Bio-IT Project co-coordinator) Toby Gibson (EMBL Group Leader) Few Mentions: Norman Davey, Aidan Budd, Konrad Förstner, Marc Gouw, Jean-Karim Heriche, Florian Huber, Charles Girodot, Jelle Scholtalbers, Grischa Toedt, Bernd Klaus, Matt Rogon, Eva-Maria Geissen, Mike Smith, Michael Wahlers, Jure Pecar, Markus Fritz, Thomas Hoffmann, Jonas Hartmann, Holger Dinkel, Frank Thommen, IT-Services, Wolfgang Huber, Members of Gibson, Zeller & Bork groups PhD Project • Konrad Förstner • Charlotte Michaux • Caroline Taouk • Bioinformatics Core Unit • Prof. Jörg Vogel • Prof. Thomas Dandekar • Ana Eulalio