(This content is outdated.)
My research interests
(Still to be written.)
Generally convenient links
- Link to Paulsson lab methods on openwetware.
- Link to Bullet Journal, a way to organize tasks and your calender. (I use a modified version, but the general concept is useful.)
- Passion Planner offers similar and extended functionality to Bullet Journal.
Journals currently followed at journal club
- Nature
- Science
- Cell
- PNAS
- PRL
- PRE
- Biophys J
- Science Signalling
- MSB Mol Sys Biology
- Nat Struct& Mol Biology
- Nature Biotechnology
- Nature Genetics
- Nat Cell Biology
- Nature Methods
- Cancer Cell
- PLoS one
- PLoS Genetics
- PLoS Biology
- Current Biology
- Physical Biology
- J. Bact.
Journals that are also interesting:
- Current opinion in microbiology
- eLife
- Trends in microbiology
- Nature Microbiology
Journals without RSS that are interesting
- MBoC, Molecular Biology of the Cell
Interesting papers
(..) Note to self: also add description
Convenient links
E. coli
- http://ecocyc.org/
- http://ecocyc.org/overviewsWeb/celOv.shtml
- http://ecoliwiki.net/
- http://www.genome.jp
- Ecocyc Sugar and Polysaccharides degradation.
- http://porteco.org/
- http://pax-db.org/#!proteins?ids=4736943,4736767,4738207
General Science
- http://nic.ucsf.edu/FPvisualization/, list and info on fluorescent proteins.
Statistics
- http://www.nature.com/collections/qghhqm/pointsofsignificance.
- http://www.nature.com/collections/qghhqm/resources.
Recombinant DNA
- http://blast.ncbi.nlm.nih.gov, website to do BLAST searches, i.e. find any genetic sequence in known genomes.
- http://www.ebi.ac.uk/Tools/msa/clustalw2/, clustalW alignment software (online), don’t forget to select DNA/protein option (and create reverse complement for reverse primer if applicable, see below).
- http://www.bioinformatics.org/sms/rev_comp.html, create reverse complement of DNA.
Software
- Python(x,y)
- gedit
- Putty (command line ssh accessing remote locations, specifically Ubuntu machines)
- WinSCP (browsing remote locations, specifically Ubuntu machines)
- TeXnicCenter, LyX
- (Windows Powershell)
- Windows grep
- Autohotkey
- Inkscape
Documentation
Other
- http://pax-db.org/#!proteins?ids=4736943,4736767,4738207
- https://bitbucket.org/
- http://bcs.whfreeman.com/lodish5e/default.asp?s=&n=&i=&v=&o=&ns=0&t=&uid=0&rau=0, repository of Lodish images.
- http://www.sporcle.com/search/?p=1&s=amino+acids, practice amino acids.
Personal links
- http://feedly.com/index.html#category%2FTans%20group%20feed, the reader I use to keep up to date with scientific articles.
- http://intranet.amolf.nl/services/ict/software/matlab/, the list of people using Matlab licences at AMOLF.
- https://intranet.tudelft.nl/en/services/fmreict-psc/network/remote-access/weblogin-citrix/, TU Delft remote access.
- https://blackboard.tudelft.nl/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1, TU Delft Blackboard.
- https://webmail.tudelft.nl/, TU Delft webmail.
- http://uba.uva.nl/en/home, UvA library.
Links with some convenient specific info
- http://stats.stackexchange.com/questions/22718/what-is-the-difference-between-linear-regression-on-y-with-x-and-x-with-y/22721#22721, about correlation coefficients I.
- http://stats.stackexchange.com/questions/32464/how-does-the-correlation-coefficient-differ-from-regression-slope, about correlation coefficients II.
Some other convenient sites
- http://biorxiv.org/
- http://arxiv.org/
Things to still learn
– Bayesian statistics. (Start by this random Google hit?)
– Time series analysis. Recommended material by SH: for non linear analysis article Interdisciplinary application of nonlinear time series methods (Schreiber 1998); for linear analysis book Time Series Analysis: Forecasting and Control (Box and Jenkins).
– Machine learning. Recommended material by SH: scikit-learn & book Machine learning: a probabilistic perspective (Murphy).
– Neural networks. Related to machine learning, also python packages available (e.g. scikit-learn or tensor flow).
– Julia. Programming language. Claims best of both C and Python worlds.
Recommendable books
On the shelves:
