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Commits (148)
# Development work discussion
Time: Mondays 11:00
Location: T-0-012
Location: T-0-008
Exceptions:
date | location
:-- | :--
May 8 | V-4-22
May 15 | T-0-008
May 22 | S-0-019
June 12 | S-0-019
September 18 | T-0-008
September 25 | t.b.a.
October 2 | T-0-008
October 9 | t.b.a.
December 11 | T-0-008
November 5 | T-0-22
See the [schedule](schedule.md) for previous and upcoming presentations.
## List of topics
In our kick off meeting, we identified a number of topics, this list may grow.
......@@ -35,6 +28,13 @@ In our kick off meeting, we identified a number of topics, this list may grow.
- Databases.
- Development models (pair programming, Agile, etc.)
- General discussion about active projects.
- Git flow.
- Maven.
- The how/what/why of logging.
- Design philosophy.
- Front-end development stack.
- Coding katas.
- Geb for browser automation in testing.
## Format
......@@ -53,24 +53,6 @@ meeting.
time | topic
--: | :--
11:00 | Presentation of a specific project.
11:20 | General discussion on a specific topic.
11:40 | Identify new topics for upcoming meetings, appoint moderator and discussion leader.
11:20 | Identify new topics for upcoming meetings, appoint moderator and discussion leader.
11:30 | General discussion on a specific topic.
11:50 | Questions and closing remarks.
## Schedule
- May 8.
- [Binary file parsing](presentations/presentation.pdf) by Jeroen. Ruben moderates.
- Discussion about GPU / Hardware. Mark S.
- May 15.
- Amegilla (lecacy system wrapper) by Sander. Bowo moderates.
- Development models.
- May 22.
- Task scheduling with Celery (Bowo). Mark K. moderates.
- Visualisation tools.
- May 29.
- Algorithm development topic by Jonathan. Mihai moderates.
- Debugging.
[Presentation Notebook](https://git.lumc.nl/wgallard/VisualizationExamples/ipython_notebook/master/bokeh_overview/bokeh_overview.ipynb)
\ No newline at end of file
# Schedule
Presentations from [2017](schedule_2017.md).
- Jan 8.
- [Evolutionary Architectures](http://nealford.com/downloads/Evolutionary_Architectures_by_Neal_Ford.pdf) (Mark S.)
- Jan 15.
- [VDE with suffix arrays]() ().
- Jan 22:
- [BBMRI meta-database schema (permission required)](https://git.lumc.nl/rp3/RP3_RP4_combined_schema) (Davy)
- Jan 29:
- [Interactive data visualization application for gene expression]() (Stephen Pieterman).
- Feb 5:
- [WDL pipelines](https://git.lumc.nl/rhpvorderman/wdl-presentation) (Ruben).
- Feb 12:
- Graph databases / triple stores (Mark T.)
- Feb 19:
- [Refactoring Mutalyzer](presentations/development-wd-2018-02-19.pdf) (Mihai)
- Mar 5:
- Spark Dataframes (Peter van 't Hof)
- [Slides](presentations/Dev-meeting_05-03-2018.pdf)
- Added slide for how to start spark on shark
- Mar 12:
- AI and variant classification.
- Mar 19:
- Asynchronous I/O in Python (Bowo)
- Mar 26:
- Singularity (Jeroen de C.)
- April 9:
- Neural networks in practice (Sander)
- April 16:
- WDL (Leon)
- [Notes of LUMC-EMC/CCBC Snakemake meeting](https://docs.google.com/document/d/1aU_yLOYlGfKyZdMUzb7E5-hOr57Y_W1ERgdqu5Qmh68/edit#heading=h.p7tyd9hathx9)
- [SASC WDL pipeline repo](https://github.com/biowdl)
- April 23:
- Discussion on future topics (AI).
- May 14:
- Web tokens (Sander).
- May 28:
- Automated Conda releases / continuous deployment (Ruben).
- June 4:
- Brainstorming AI applications in Genomics (Jeroen/Peter/Sander/Leon/Guy)
- June 11:
- [Single Sign-On with SAML](presentations/sso_development_11_june.pdf) (Mark)
- June 18:
- Encode pipelines (Dani).
- October 8:
- New functionalities in Python 3 (Sander).
- October 15:
- [HGVS parsing](presentations/MLefter_hgvs_parser_2018-10-15.pdf) (Mihai).
- October 22:
- Structuring programs in QT.
- October 29:
- Open Source software licensing and compatibility (Bastian).
- November 5:
- Discussion on Ansible deployment (structuring, best practices.)
- November 12:
- Guest lecture.
- November 19:
- Knowledge management systems (Ruben).
- November 26:
- BIOS database and RDF (Leon / Rajaram).
- December 3:
- Off topic (Jonathan).
- December 10:
- JOSS (Jeroen).
- December 17:
- ~~Slack alternatives (discussion).~~ (Postponed due to lack of participants)
- January 7:
- Slack alternatives (discussion).
- January 14:
- Education portfolio.
- Upcoming.
- Continuous integration (Ruben)
- STR extraction (Jonathan)
- Regulations for medical devices (Alex Vernooij)
- Kubernetes.
- Block chains.
- DTL / RSE.
- Formal languages / grammars.
- Invite people from imaging/radiology.
- Microscopy / Fons Verbeek.
- Invite people from proteomics.
- Invite people from LCBC.
- Ontologies.
- Security / privicy issues (GDPR).
- Packaging in general.
- Development cycle.
- Main purposes of programming languages.
- General purpose GPU computing.
- Applied machine learning with SK-learn / scikit (Guy)
- Complexity theory
- RISC-V and tiny FPGA
- Notes.
- Generic topics, but with a link to current activities.
- Technical details of methods, applications more to NGS meeting.
- Room for pure theory.
\ No newline at end of file
# Schedule 2017
- May 8.
- [Binary file parsing](presentations/JLaros_Binary_file_parsing_08-05-17.pdf)
by Jeroen. Ruben moderates.
- Discussion about GPU / Hardware. Mark S.
- May 15.
- [Amegilla](presentations/SanderBollen_Amegilla_15-05-17.pdf) (lecacy system wrapper) by Sander. Bowo moderates.
- Development models.
- May 22.
- [Task scheduling with Celery](presentations/WArindrarto_Task_Execution_with_Celery_22-05-17.pdf)
by Bowo. Mark K. moderates.
- Visualisation tools.
- May 29.
- [The Future of the Variant Description Extractor](presentations/JVis_Future_of_VDE_29-05-17.pdf)
by Jonathan. Mihai moderates.
- Debugging.
- June 12.
- [Webdriver testing](presentations/MKroon_webdriver_testing_12-06-17.pdf) by Mark K. Guy moderates.
- Integrated testing frameworks.
- June 19.
- [Bokeh](https://git.lumc.nl/wgallard/VisualizationExamples/ipython_notebook/master/bokeh_overview/bokeh_overview.ipynb) Guy. Jonathan moderates.
- Evaluation of previous meetings.
- June 26.
- [Nested and Javascript](presentations/Mark_Santcroos_Nested_Javascript_26-06-17.pdf) by Mark S. Jonathan moderates.
- Choosing front end JavaScript frameworks.
- September 4.
- [Tips on how to work with docker and ansible (Ruben)](presentations/galaxy-docker-ansible.pdf)
- September 11 / September 25.
- [Spark](https://spark.apache.org/) (Peter) [Slides](presentations/Peter_Spark-11-09-2017.pdf)
- October 2.
- Rust for safe and efficient programs (Bowo)
- October 9.
- [Pattern recognition](presentations/Pattern_Recognition_Sander_Bollen.pdf) (Sander)
- October 16.
- [Roadmap BioPet](presentations/Developer_WD_2017_10_16.pdf) (Leon)
- October 23.
- [Clustering](https://git.lumc.nl/bvhhornung/Presentations/uploads/06bf6627f491d0aadd372c7bdd177e7c/clustering.pdf) (Bastian)
- October 30.
- [SQLAlchemy](presentations/MLefter_SQLAlchemy_Introduction_2017-10-30.pdf) (Mihai)
- November 6.
- [Deep learning](presentations/deep_learning.mkroon.20171106.pdf) (Mark K.)
- November 20.
- [ELK stack](presentations/Mark_Santcroos_ELK_20-11-17.pdf) (Mark S.)
- November 27.
- Documentation automation (Ruben)
- December 4.
- PhenoMeNal platform with a Galaxy and Kubernetes back-end (Michael van Vliet, m.s.vanvliet@lacdr.leidenuniv.nl)
- December 11.
- [X.509](presentations/jvis_x509.pdf) (and other) auth methods (Jonathan)