Contact info joel.ostblom@protonmail.com, LinkedIn.

Credentials GitHub, GitLab, StackOverflow, Sourcerer.

Professional Experience

Course Creator
since Dec 2019
University of Toronto
Co-developed and TAed the graduate level course Coding for Biomedical Engineers. Focus on learning Python for data analysis.
Teaching Assistant
since Jan 2019
University of British Columbia
Assisting in three courses in the Masters of Data Science (Data Visualization; Data Wrangling; Privacy, Ethics, and Security), including leading a group of fours TAs for Data Visualization and assisting with content development for Data Wrangling. Created and taught a one hour seminar on intermediate pandas. Recognized with a TA award for outstanding work.
Instructor
since Jun 2018
Datacamp
Developed two teaching projects on data-wrangling, supervised and unsupervised learning using Python and R.
Data Science Intern
May 2019 - Dec 2019
Neurio
Clustered households based on energy consumption patterns to improve modelling strategies and to create consumer incentive for lower energy usage through gamification. Created interactive dashboards for internal use and learnt about project structure and code design.
Course Coordinator
2017 - 2018
Department of Ecology & Evolutionary Biology & UofTCoders
Lead the development of and taught a 4th year undergraduate course on open, reproducible data practices with R, which was positively received and incorporated into the departments long-term curriculum.
Workshop Instructor
2017
Digital Humanities Network & UofTCoders
Taught graduate students intro to computing and programming with Bash.
Data Analyst
Mar 2016 - Dec 2016
Ghana Medical Health
Analyzed operational and market data. Published visualizations of the results in the end of year report to donors.

View all professional experiences By default only the most relevant entries are shown. Click here to reveal all.

Platform Developer
Feb 2015 - Oct 2015
FundingFinder (startup)
Designed an early prototype of a university scholarship SQL database & query form.
Research Assistant
Jul 2015
Tokyo Systems Biology Institute, Dr. Ayako Yachie
Constructed an RNA-sequencing pipeline with R (DeSeq2) & STAR and applied it to study differential gene expression in mouse stem cells.
Research Assistant
Jan 2014 - Jan 2015
Karolinska Institute, Dr. Michael Andäng
Performed bioinformatic analyses of data from various biophysical-oriented stem cell projects.
Research Assistant
Aug 2013 - Dec 2013
University of Toronto, Dr. Peter Zandstra
Refined and enhanced the software I developed during my Master thesis project.
Research Assistant
Sep 2011 - Jan 2013
Karolinska Institute, Dr. Theresa Vincent
Investigated inhibitory mechanisms for cancer stem cell growth and metastasis.
Summer Internship
Jun 2010 - Aug 2010
Karolinska Institute, Drs. Abram Katz & Håkan Westerblad
Developed an in vitro training model for mouse skeletal muscle.

Publications


Eight publications, three acknowledgements, five poster presentations, and three manuscripts in preparation.
In preparation
Johnston, Ostblom, Hassan. ROStools, I am one of the lead developers to this specification and toolkit for structured analytical workflows in open reproducible scientific projects.
In preparation
Wilson et al. Merely Useful, I am one of the main contributors to this learning resource on introductory data science and software engineering, which is equivalent to two semester-long courses.
Jun 2019
Johnston, Bonsma-Fisher, Ostblom et al. A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching. Journal of Open Source Education, DOI: 10.21105/jose.00049.
Jan 2019
Ostblom et al. Context-explorer: Analysis of spatially organized protein expression in high-throughput screens, PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1006384. Awarded “editor’s pick” among all PLOS journals in the open source toolkit section.
Apr 2017
I was mentioned in the acknowledgement section for programming training and data analysis advice for Shukla et al. Progenitor T-cell differentiation from hematopoietic stem cells using Delta-like-4 and VCAM-1, Nature Methods, DOI: 10.1038/nmeth.4258.

View all publications By default only the most relevant entries are shown. Click here to reveal all.

Oct 2019
Tewary, Dziedzicka, Ostblom et al. High-throughput micropatterning platform reveals Nodal-dependent bisection of peri-gastrulation–associated versus preneurulation-associated fate patterning, PLOS Biology, DOI: 10.1371/journal.pbio.3000081.
Mar 2019
Thavandiran, Hale, Blit, Sandberg, McElvain, Gagliardi, Sun, Witty, Graham, Mcintosh, Afshar, Le, Ostblom et al, Functional arrays of human pluripotent stem cell-derived cardiac microtissues, BioRxiv.
Jan 2018
Yachie-Kinoshita, Onishi, Ostblom et al. Modeling signaling-dependent pluripotent cell states with boolean logic can predict cell fate transitions, Molecular Systems Biology, DOI: 10.15252/msb.20177952.
Dec 2017
Tewary, Ostblom et al. A stepwise model of Reaction-Diffusion and Positional-Information governs self-organized human peri-gastrulation-like patterning, Development, DOI: 10.1242/dev.149658.
Dec 2013
Nazareth, Ostblom et al. High-throughput finger-printing of human pluripotent stem cell fate responses & lineage bias, Nature Methods, DOI: 10.1038/nmeth.2684.
Oct 2012
Sekyrova, Ostblom, Andäng. Blebbing as a physical force in cancer EMT: Parallels with mitosis, Seminars in Cancer Biology, DOI: 10.1016/j.semcancer.2012.05.007.

Acknowledgements

Jul 2018
Content review & feedback of a book on how to effectively teach computational topics: Greg Wilson (ed.): Teaching Tech Together. Lulu.com, 2018, 978-0-9881137-0-1
Jun 2015
Content review, literature research and discussions for Onishi & Zandstra LIF signaling in stem cells and development, Development, DOI: 10.1242/dev.117598.

Poster Presentations

May 2019
BC RegMed Adherent pluripotent stem cells recapitulate symmetry breaking cell fate acquisitions of differentiating three-dimensional cell aggregates (2nd place poster prize)
Nov 2017
Till & McCulloch Meetings meetings Spatially organized gene expression heterogeneity in mouse pluripotent stem cells
Jun 2015
International Society of Stem Cell Research Annual Meeting Emergence of distinct spatial expression patterns in human pluripotent stem cell colonies of confined sizes
Jun 2014
International Society of Stem Cell Research Annual Meeting ContextExplorer - Exposing spatial organization of phenotypic heterogeneity in human pluripotent stem cell colonies
Apr 2014
Scientific Day, Institute of Biomaterials & Biomedical Engineering ContextExplorer: Exposing spatial organization of phenotypic heterogeneity in human pluripotent stem cell colonies

Education

Ph.D. Biomedical Eng.
since Jan 2014
University of Toronto, Dr. Peter Zandstra
Thesis: Investigating transcriptional heterogeneity among pluripotent stem cells and developing software for novel analysis methods of high content imaging data.
Courses: Stem cell engineering, cognitive foundations for effective leadership, bioengineering, applied bioinformatics.
M.Sc. Biomedicine
Aug 2011 - Aug 2013
Karolinska institute, Drs. Peter Zandstra & Michael Andäng
Thesis 2nd year: Developed analysis software and applied it to highlight how the microenvironment impinge on early stem cell fate decisions.
Thesis 1st year: Identified key genes in cell cycle driven gene expression fluctuations in pluripotent stem cells.
Courses: Stem cells & regenerative medicine, bioinformatics, biostatistics, biomedical communication, entrepreneurship.

View all academic degreesBy default only the most relevant entries are shown. Click here to reveal all.

B.Sc. Biomedicine
Aug 2008 - June 2011
Karolinska Institute, Drs. Prasanna Kolatkar & Larry Stanton
Thesis: Increased the reprogramming efficiency of fibroblasts five-fold through single amino acid mutagenesis of Sox17.
Courses: Stem cell biology, immunology, neuroscience, cell biology, biostatistics, physiology, molecular oncology, biochemistry.

Soft Skills

Instruction
2019
University of British Columbia Master of data science
Two days of lectures and hand-on training on effective teaching.
Teaching Assistance
2018 & 2019
University of Toronto & University of British Columbia
Two lectures on how to communicate with students and resolve conflicts.
Openness
2018
Mozilla Open Leadership Program
Four months mentorship and training on how to work openly and lead open access projects. Lead a global sprint session for my project with several contributors.
Teamwork
2018
MITACS Essentials of productive teams
A one-day hands-on course on how to participate in and lead an effective team unit.
Project Management
2018
MITACS Foundations of Project Management 1 & 2
Four days of hands-on courses on project management, team dynamics and leadership.
Leadership
2016
University of Toronto
One semester course in the cognitive and psychological foundations of effective leadership

View all soft skillsBy default only the most relevant entries are shown. Click here to reveal all.

Commercialization
2016
NSERC M3 Create
A two-day workshop in public speaking, collaboration, negotiation and IP/patent law.
Prewriting
2013
University of Toronto
Several lectures on strategies for developing & organizing ideas

Extracurricular Merits

Dashboard Developer
since 2018
Built an interactive Bokeh dashboard for visualization and clustering of nutritional data to facilitate comparison of food items (wait for the page to load initially).
Data Science Teacher
since 2016
Created several narrative teaching notebooks for data science.
Infrastructure Manager
since 2016
University of Toronto
Responsible for evaluating and purchasing $400,000 imaging and computational equipment (saving $600,000 compared to competing suggestions). Setup and management of the lab’s computational infrastructure, including three Linux workstations, the lab’s Google Suits account and folder structure, identifying proper backup solutions for ~100TB data, and designing a data management plan.
Open Source Contributor
since 2015
Created context-explorer and to aggregate and visualize high throughput microscopy data, spiral-tile to stitch and normalize microscopy images, and sinfo as a minimal measure to increase reproducibility of Jupyter notebooks and facilitate version reporting in general. Minor contributions to several scientific Python packages (plotly, seaborn, pandas, matplotlib, jupyterlab, shap, holoviews, jupytext), zotero-cli, the ranger file browser, vim-pandoc, vim-rmarkdown, csv.vim, pdf-annots, phageParser, python java-bridge, and the Python social sciences data carpentry lecture.
Student Supervisor
2019
University of British Columbia
Mentored two incoming PhD students, one during ten months and the other for a four months summer project. Taught wetlab techniques, microscopy imaging, data analysis, presentation skills, and scientific writing.
Session Instructor
2018
University of British Columbia
Created a tutorial on interactive, reproducible reporting of scientific results using Jupyter Notebooks and plotly express. Taught as a two hour session for graduate students and postdocs.
Host & Mentor
2018
Mozilla Open Leadership Program
Hosting sessions for 30 participants and mentoring one student in how to work and lead open projects during the Open Leadership program.
Workshop Developer
2018
UofTCoders
Lead the content development for three 2-day workshops on using Python for reproducible data analysis (based on data carpentry). Co-taught each session to ~30 participants.
Workshop Instructor
2017-2018
UofTCoders & The Carpentries
Taught graduate students at six workshops. Topics including automation via the Unix shell, programming with Bash, & data analysis and visualization in Python.
Session Instructor
2017-2018
UofTCoders
Taught eight sessions for graduate students with topics including bash, Python, data analysis and visualization, vim, pandoc, and tmux.
Guest Lecturer
2017
University of Toronto, APS106
Taught high level overview of image analyses with Python.
Teaching Volunteer
2015-2017
Let’s Talk Science & Stem Cell Talks
Taught basic stem cell science to high school students, elementary students, kids, and parents (four separate occasions).
Teaching Volunteer
2016
University of Toronto
Taught high-throughput microscopy & image analyses to undergrads as part of BME346H1-Omics.
Case Finalist
2016
IMS Brogan
Performed data analysis in a team of three for a consulting case competition. We reached the final round and were accredited as the team with the most data-driven insights.
IT & Education Lead
2015 - 2016
Engineering World Health UofT Chapter
Involved in founding the UofT student chapter and lead the IT and Education teams. We received the chapter of the year award 2016.
Student Supervisor
2014
University of Toronto
Co-supervised a 4th year thesis student, primarily in data analyses techniques of high throughput imaging data.
Study Buddy
2013
Stiftelsen Läxhjälpen
Assisted students in socio-economically vulnerable areas to increase their high school enrollment rates.

View all extracurricular merits By default only the most relevant entries are shown. Click here to reveal all.

Topic Expert
since 2019
Mozilla Open Leadership Program
Available to provide support as needed for participants in the open leadership program.
Workshop Helper
2017-2018
UofTCoders & The Carpentries
Assisted at seven workshops for graduate students. Topics included Unix, git & GitHub, image analysis, data analysis in R & Python.
Student Ambassador
since 2014
Karolinska Institute
Assisting exchange students from Karolinska Institute at the University of Toronto.
Translation Volunteer
2015
SCOPE
Translated stem cell blog post to Swedish.
Vice President
2012
Biomedical Student Section
Coordinated program-wide activities to improve the student environment.
Board Member & Webmaster
2011
BRO
Worked to connect Biomedical students across Sweden.
Board Member
2010
Biomedical Program Committee
Assisted in program development to improve the education at Karolinska Institute.
Team Captain (C & A)
1995 - 2003
Provided leadership at youth and competitive levels. Played in the Swedish J20 SuperElit division and ACHA college hockey in the US 2006-2008.

Awards


Total amount awarded: CAD 135,000
TA Award
2019
University of British Columbia
For outstanding contributions to the Master of data science program.
NSERC M3 Create
2015 & 2018
Natural Sciences & Engineering Research Council of Canada
To streamline translational research training among students.
International Scholar
2014-2017
University of Toronto
In support of excellent international students at IBBME, University of Toronto.
Gålö Higher Education
2014 & 2016
Gålö Foundation
In support of outstanding students participating in higher education outside of Sweden.

View all awards By default only the most relevant entries are shown. Click here to reveal all.

Loo Geok Award
2015
University of Toronto
For outstanding academic achievement & extra-curricular leadership.
Milligan Award
2014
University of Toronto
In recognition of the student’s research accomplishments.
Essay Award
2013
Karolinska Institute
Second place exchange studies essay competition.
INK Scholarship
2013
Karolinska Institute
Master Thesis exchange studies in Toronto.
Research Scholarship
2011-2013
Karolinska Institute
Support for part time research in parallel with my Master studies.
INK Scholarship
2011
Karolinska Institute
Support for Bachelor Thesis exchange studies in Singapore.
Inspirational Poster
2011
Karolinska Institute
Master thesis poster selected as inspirational poster for incoming students.
Inspirational Article
2009
Karolinska Institute
Summer internship article selected as inspirational article for incoming students.
Research Scholarship
2009
Karolinska Institute
Financial support for summer laboratory internship.