BioRender

BioRender is a tool for creating professional-looking science figures in minutes using templates and over 20,000 stock icons from 30+ areas in the life sciences using a web-based, drag and drop interface. The following figure is one of many templates; each element in the template is a simple icon.

BioRender App

Icons

BioRender contains an immense library of science-themed, simple icons including: cell structures and types, anatomy, different biomolecules, lab equipment, membranes and many different species from the simple to the complex. Have your own data you want to include in the figure? You can drag and drop images from your computer’s file system onto the canvas, they’ll appear as icons. Need something that is not in the library? With a paid subscription, you can ask BioRender to create new icons.

The simple icons in the library can also be grouped into compound icons in the same way that objects can be grouped (and ungrouped) in most drawing programs. A third type of icon, the bio-brush is unique to BioRender.

One of my favorite features is the bio-brush. If an icon has a brush icon, you can use the bio-brush feature to draw repeating sequences of the icon, complete with the ability to make curves. Imagine drawing a lipid bilayer, a layer of cells or a string of nucleosomes as easily as drawing a line. Drawings that would take hours in a normal drawing program can be done in seconds with BioRender. For an example, see this BioRender tutorial for a demonstration of the membrane brush and a vessel brush.

Schematic of membrane disruptive and non-membrane disruptive bacterial killing mechanisms of AMPs Illustration created with BIORENDER.COM.
Membranes can be drawn with a membrane brush and then ungrouped to form a break into which additional elements can be added. Figure taken from https://www.researchgate.net/figure/Schematic-of-membrane-disruptive-and-non-membrane-disruptive-bacterial-killing-mechanisms_fig3_336372513.

The Biorender Learning Hub has a lot of videos on topics such as design, learning, usage and customization. This in combination with the intuitive interface means that the user can make professional-looking figures in an afternoon. Another feature is the ability to make and present slides within the BioRender interface; shared work spaces are planned.

The free license gives you the right to use the figures you create for educational purposes and in grants. If you want to publish your figures in journals or use your figure for commercial purposes, you need to upgrade to the commercial license which is $35 per month for individuals or $99 per month for a group of up to 5 members (in October 2021). Institutional licenses are also available.

Are there any negatives? The interface is optimized for Chrome so if you’re not using Chrome, there may be some issues. The price is steep to keep a permanent license if you don’t have a research budget but even a student can cough up 35 dollars to buy a month-long license to make their final figures right before submitting.

Resources for learning German

Preply online tutoring from native speakers at good prices

Deutsch Einstufungstest and C1 course

Exercises on different levels

Goethe institute

Herr Professor’s podcast juggles one verb per day, the right amount and very well done. His list of tools and treatise on articles are also helpful.

News in slow German has many resources in addition to news read slowly.

Festung Aarburg, Olten – Aarburg – Olten, July 18 2020 with Korinna

Festung Aarburg

During my daily commute from Zurich to Bern, I often noticed a big castle positioned on the Aare River. Finally, after 9 years of commuting I finally visited with a friend. This hike from Outdoor Active is a easy stroll from Olten to Aarburg, followed by a 7 kilometer hike including a 250 meter ascent to the Sälischlössli and a pass by an animal park on the way back to Olten. We included a visit inside the Festung Aarburg, an old castle which is now in use as a Jugendheim (Juvenile Detention Center) for boys aged 16-20. For this reason, visiting the castle is limited and currently, there is only one 1.5 hour tour per week on Saturdays at 14:00 (in Swiss German). It was well worth the visit.

The walk to Aarburg is along the Aare by meadows, train tracks and farms.

On the path to Aarburg from Olten, the Sälischlossli, a rebuilt castle with a restaurant, can be seen across the river at the peak of the first hill.
The view from a distance shows the size and location of the Festung Aarburg.

At 14:00 on Saturdays, the Festung Aarburg is open for a guided tour in Swiss German (cost 10 CHF). The guide explains the castle’s construction history, life in the castle, how the rooms were used and a bit of how it is used today as a juvenile detention center for boys aged 16-20. The fortress, strategically located at a narrow point of the Aare River, is built into a massive spur of rock with steep walls on the outside.

After the castle visit, we continued to the Sälischlössli, a small castle with a restaurant built in 1870/71 as an expansion of a castle ruin. After the walk up, the Restaurant Sälischlössli is a relaxing place to have an ice cream (or french fries) and a great view.

The way home passes by an animal park. Unfortunately, the raccoons were not out but we did find some handsome deer.

Hike near Lauterbrunnen Wengen: Gimmelwald – Sefinental – Stechelberg

Friday, June 26, 2020

This 11.5 km hike from outdooractive.com has a gentle 200 meters up followed by 900 meters down. Travel started with a train from Bern to Interlaken Ost, another train to Lauterbrunnen, followed by a gondola to Grütschalp, and finally another train to Mürren, the starting place of the hike. Highlights include views of the Eiger, Monch and Jungfrau, many waterfalls including at one point the trail going behind a waterfall and an old water-powered sawmill.

View of the Eiger, Mönch and Jungfrau from the train to Mürren
View at the start of the hike
Town of Gimmelwald
The number and variety of wildflowers was amazing.
This old sawmill is in the Sefinental. Powered by water, it is still functional as seen in this video.
Stop for a rest and a foot bath in the ice-cold water.
Thanks for the hike, Marta!

Want to feel better about population growth?

This video by Hans Rosling from the Gapminder Foundation paints a portrait of population growth that is less bleak than most people intuit. The video doesn’t address climate change but it does convince that population growth is not an unsolvable problem, nor will population increase always be exponential. Using population data collected from different countries, he shows how population growth is projected to level off at 11 billion people.

Achieving a state of the world that can sustain 11 billion people is not out of the realm of possibility. If resources are used wisely, sustainably, and shared somewhat fairly, the earth can accommodate this population size. He says at the end of this video that he is not an optimist but also not a pessimist. He is a possibilist, meaning he knows what is possible and works toward the best possible outcome. One way to feel better while being inundated with an overwhelming amount of pessimistic news is to get involved in local politics, vote and work towards sustainability both at home and in coordinated actions. Put your energy toward the possible!

Bern Restaurants

Du Nord SG’s and my favorite restaurant in Bern, nice chill atmosphere with good food
Royal Asian good food at a good price, 10 CHF for lunch
Kloesterli Weincafe nice food and wine, excellent polpo
Tre Fratelli I had a homemade pasta with seafood, really yummy, would bring my Italian relatives.
Restaurant at the Alpine Museum nice lunch place, fills and some plates sell out, good secret tip for lunch in Bern, Helvetiaplatz 4, reserve +41 31 331 22 22
Restaurant Commerce good food in a homey atmosphere, one of those restaurants where it seems like nothing has changed in many a year
Fugu Nydegg Thai & Japanese restaurant. The owners are Thai, so better stick with Thai … and spicy really means spicy
Essort great lunch but also excellent in the evening
Metzgerstuebli

Zurich Restaurants

Restaurants in ZuriNord

My Kitchen My new favorite Malyasian with severely delicous Malaysian bread, Roti Canai. moved out of Oerlikon
Restaurant Kerala really nice Indian by Radiostudio
Asiaway Holy Cow! Some of their food is really fantastic. Fresh herbs and lovely sauces. Oerlikon has some great restaurants.
Dapur Indonesia tastes excellent but a bit expensive for what you get
Schnitzelhuus If you want a good schnitzel, this is the place to come. Portraits of Austrian and French royalty is the decor. Sometimes the staff wear traditional clothes which makes for a nice atmosphere for visitors.
Cheyenne The food isn’t the best in the world but sometimes we like to eat in an American atmosphere. It is like a sports bar so it can get loud inside. In the summer, it is a nice place to sit outside.
Giesserei Good Restaurant in Oerlikon, pricey
Rolli’s Steakhouse Our birthday standard, good steak served on a hot stone, reserve at least a week in advance
Stadionli restaurant at the Kunsteisbahn Oerlikon Siewerdstrasse 80 043 333 49 14 ; The restaurant belongs to the Ice Skating Rink so you would think the food would be terrible but the nightly specials are excellent.
Il Postino pizza close to Irchel Park
Fine Choice Next to the Burger King in Oerlikon, when we want to eat something fast and cheap we get the veggie noodles here
Coopers Pub for when you need a pint o’ Guiness

Restaurants in Zurich

Restaurant Joseph our current favorite, small plates of food so 4 or 5 make a delicious dinner for around 80 CHF per person Our current favorite restaurant 4 or 5 small plates for 80 CHF, really great food
Cheti’s Curry Indian and Sri Lankan Food, very very good curry, owner is a nice person too, Seefeldstrasse 7A 8008 Zurich Tel: 043 268 55 85
The Bombay Store Stampfenbachstr. 32 8006 Zurich 079 200 14 18 Good cheap Hallal Pakistani food for 15 SFr per plate
India Street Food Sri Lankan, Indian food. Langstrasse 213 8005 Zurich, woo, samosas and other tasty deep-fried hand held food for 3 CHF each. Mo – Sa 11:30-23:30
Sternen Grill at Bellevueplatz täglich 07:00-24:00 – the best bratwurst stand, i buy their mustard.
Palmhof now changed into an ale house (Alehouse Palmhof) with a good beer selection (food is ok). The old Palmhof was unique, what a loss that it is gone. I’m keeping it on my list as a memory. Universitätstrasse 23 8006 Zürich
Hot Pasta near the ETH main building, good pasta at a decent price, not big portions so big guys have to stop at McDonalds after
Samurai – best sushi I have had in Zurich, Weststrasse 180, 8003 +41-43-811-5678
Ah-Hua Good Thai for 18-20 SFr per plate. Brauerstrasse 9 8004 Open from 11-21 Uhr. 01 241 39 37 I make Homer Simpson noises when i think of this place. There is another one at Helvetiaplatz, requires reservation
Restaurant Schlauch Münstergasse 20 ObereZäune 17 Niederdorf good organic Swiss food for about 20-25 Sfr per plate. Lots of pool tables too.
Baur au Lac Talstrasse 1. 01 220 50 20 Best Sunday brunch with a fantastic dessert bar. It costs around 85 Sfr so go hungry. Reservation required.
Der gruene Libanon Lebanese kebobs by the main train station
Mohrenkopf Niederdorfstrasse 31, my favorite cafe in zurich, they have good food, nice coffe and their speciality are Mohrenkopfs, marshmallow inside and chocolate outside
Reithalle Gessnerallee 8 nice place to eat and sit outside in the summer
Restaurant Hirslanderhof Geheimtip Forchstrasse 76, 8008
Restaurant Rigiblick One of the best dining experiences I have had, everything was tip top, lunch menu took 2.5 hours for 4 courses
Restaurant Cedre Everyone’s favorite Lebanese Restaurant, Badenerstrasse 78 8004 Zurich 044 241 4272, needs a reservation, really great food

The Bombay Store Karachi Stampfenbachstr. 32 8006 Zurich 079 200 14 18 Good cheap Hallal Pakistani food for 15 SFr per plate
India Street Food Sri Lankan, Indian food. Langstrasse 213 8005 Zurich, woo, samosas and other tasty deep-fried hand held food for 3 CHF each. Mo – Sa 11:30-23:30
Sternen Grill at Bellevueplatz täglich 07:00-24:00 – the best bratwurst stand, i buy their mustard.
Palmhof now changed into an ale house (Alehouse Palmhof) with a good beer selection (food is ok). The old Palmhof was unique, what a loss that it is gone. I’m keeping it on my list as a memory. Universitätstrasse 23 8006 Zürich
Hot Pasta near the ETH main building, good pasta at a decent price, not big portions so big guys have to stop at McDonalds after
Samurai – best sushi I have had in Zurich, Weststrasse 180, 8003 +41-43-811-5678
Ah-Hua Good Thai for 18-20 SFr per plate. Brauerstrasse 9 8004 Open from 11-21 Uhr. 01 241 39 37 I make Homer Simpson noises when i think of this place. There is another one at Helvetiaplatz, requires reservation
Restaurant Schlauch Münstergasse 20 ObereZäune 17 Niederdorf good organic Swiss food for about 20-25 Sfr per plate. Lots of pool tables too.
Baur au Lac Talstrasse 1. 01 220 50 20 Best Sunday brunch with a fantastic dessert bar. It costs around 85 Sfr so go hungry. Reservation required.
Der gruene Libanon Lebanese kebobs by the main train station
Mohrenkopf Niederdorfstrasse 31, my favorite cafe in zurich, they have good food, nice coffe and their speciality are Mohrenkopfs, marshmallow inside and chocolate outside
Reithalle Gessnerallee 8 nice place to eat and sit outside in the summer
Restaurant Hirslanderhof Geheimtip Forchstrasse 76, 8008
Restaurant Rigiblick One of the best dining experiences I have had, everything was tip top, lunch menu took 2.5 hours for 4 courses
Restaurant Cedre Everyone’s favorite Lebanese Restaurant, Badenerstrasse 78 8004 Zurich 044 241 4272, needs a reservation, really great food

Cheti’s Curry Indian and Sri Lankan Food, very very good curry, owner is a nice person too, Seefeldstrasse 7A 8008 Zurich Tel: 043 268 55 85
The Bombay Store Stampfenbachstr. 32 8006 Zurich 079 200 14 18 Good cheap Hallal Pakistani food for 15 SFr per plate
India Street Food Sri Lankan, Indian food. Langstrasse 213 8005 Zurich, woo, samosas and other tasty deep-fried hand held food for 3 CHF each. Mo – Sa 11:30-23:30
Sternen Grill at Bellevueplatz täglich 07:00-24:00 – the best bratwurst stand, i buy their mustard.
Palmhof now changed into an ale house (Alehouse Palmhof) with a good beer selection (food is ok). The old Palmhof was unique, what a loss that it is gone. I’m keeping it on my list as a memory. Universitätstrasse 23 8006 Zürich
Hot Pasta near the ETH main building, good pasta at a decent price, not big portions so big guys have to stop at McDonalds after
Samurai – best sushi I have had in Zurich, Weststrasse 180, 8003 +41-43-811-5678
Ah-Hua Good Thai for 18-20 SFr per plate. Brauerstrasse 9 8004 Open from 11-21 Uhr. 01 241 39 37 I make Homer Simpson noises when i think of this place. There is another one at Helvetiaplatz, requires reservation
Restaurant Schlauch Münstergasse 20 ObereZäune 17 Niederdorf good organic Swiss food for about 20-25 Sfr per plate. Lots of pool tables too.
Baur au Lac Talstrasse 1. 01 220 50 20 Best Sunday brunch with a fantastic dessert bar. It costs around 85 Sfr so go hungry. Reservation required.
Der gruene Libanon Lebanese kebobs by the main train station
Mohrenkopf Niederdorfstrasse 31, my favorite cafe in zurich, they have good food, nice coffe and their speciality are Mohrenkopfs, marshmallow inside and chocolate outside
Reithalle Gessnerallee 8 nice place to eat and sit outside in the summer
Restaurant Hirslanderhof Geheimtip Forchstrasse 76, 8008
Restaurant Rigiblick One of the best dining experiences I have had, everything was tip top, lunch menu took 2.5 hours for 4 courses
Restaurant Cedre Everyone’s favorite Lebanese Restaurant, Badenerstrasse 78 8004 Zurich 044 241 4272, needs a reservation, really great food

zum Kropf Good Swiss food, not too expensive.
Roi-et Daniel said that this food actually uses the whole scale of hotness i.e. they might actually produce food that is too hot to eat.
Beyond Good Chinese food next to the Bahnhof, Zollstrasse 20 8005 043 355 8345
Kantorei Good Swiss food, not cheap. Neumarkt 2, 044 252 27 27
Restaurant Pergola Recommended by Markus – get some kind of fleisch for two
Brasserie Johaniter Niederdorf decent Swiss food at a reasonable price
Mere Catherine Nägelihof 3/Niederdorf – good food for about 70CHF per person for dinner, wine and dessert
Linde Oberstrass Back & Brau, Universitätsstrasse 91
Il Golosone Italienische Spezialitaeten 8001 Zuerich 01 212 40 08 Good pizza, always full. Make reservations, be on time or you will lose them.
Alpenrose 01 271 39 19 Daniel and Sophie’s favorite high-end Swiss food Reservations required. Corner of Limmatstrasse and Quellenstrasse.
Blinde Kuh Mühlebachstr. 148  Tel: (01) 421 50 50  Dining experience in complete darkness with seeing-handicapped waitpeople. a unique experience…  Must make reservations far in advance.
Restaurant Waldhaus Katzensee  Wehentalerstr. 790  the perfect family restaurant with a collection of 1-franc rides out front, a small train to ride, and a playground- all within view of an outdoor eating area.
Morgenstern Zwinglistrasse 27; 01 242 68 30 not cheap but consistently good Italian food

Fighting Unfair Collection Practices in Switzerland

A big Danke! to the Swiss Stiftung für Konsumentenschutz (SKS) for saving me 58 Swiss Francs! An unpaid bill from Ricardo that I did not see was sent to Intrum Justitia for collection.  Ricardo has some strange billing practices, namely they send (sent?) periodic bills with charges for posting items but the big bills with the fee incurred when something actually sold seems to only go to the internal Ricardo mail. I never checked this internal mail box because they were periodically sending me bills! What gives, Ricardo? Are my settings wrong? Are you complicit in this Abzockerei?

This SKS page explains what to do if you get such a bill. It also explains that Inkasso firms (in my case Intrum Justitia) are only allowed to bill you for the amount of the unpaid bill plus interest. They are not allowed to tack on a huge fee as their fee must be collected from the firm for whom they are collecting. In my case the unpaid bill was 38.65 CHF, the interest was 0.10 CHF and the Intrum Justitia fee was 58.00 CHF. I followed the instructions on the SKS page which includes a letter to send to the Inkasso firm (Musterbrief). I modified the letter to include my personal information and my numbers and sent it to Intrum Justitia registered with return acknowledgement requested.  I immediately paid Intrum Justitia the part that is legally required, i.e. 38.75. Within 5 days my Ricardo account was unblocked. After one week, I have not heard back from Intrum Justitia.

SKS will help members without cost and for non-members help is available via a 900 number. Membership is well worth the cost.

  • March 6: Letter from Intrum Justitia is dated March 6
  • March 7: I paid Intrum Justitia 38.75 and sent my letter by email to Intrum Justitia with a copy to SKS
  • March 8: I sent registered letter by Swiss Post
  • March 13: My Ricardo account was unblocked
  • March 23: I received another bill from Intrum Justitia for 58 CHF. Note that this second bill is dated March 13.
  • March 31: I send a second letter to Intrum Justitia based on the first letter.
  • May 8: I have not heard anything else from them.

Array jobs with SLURM and Singularity

Singularity containers can be used to package workflows, software, data and libraries. Some of the software packages at vital-it and unibe are housed in singularity images. These are loaded with a different syntax then the pre-exisitng modules.

#!/bin/bash

#SBATCH –mail-user=email@unibe.ch
#SBATCH –mail-type=END,FAIL

#SBATCH –job-name=”bax2bam”

# do 50 jobs labeled 01-50 and run at most 20 at a time
#SBATCH –array=01-50%20

# Runtime and memory
#SBATCH –time=08:00:00 #
#SBATCH –mem-per-cpu=8G # n
#SBATCH –cpus-per-task=1

# Partition
#SBATCH –partition=all

# use the full path to the working directory
#SBATCH –workdir=pacbio_raw

#run the instance of the software

singularity run /software/singularity/containers/PacBioSuite-6.0.0.47841-1.centos7.simg

# use a formatted print statement to pad the numbers to all have the same number of digits. “%02g” pads each number with 0’s to 2 positions

NUM=$(printf “%02g” ${SLURM_ARRAY_TASK_ID})

# the value has to be exported to the singularity instance
export NUM

#execute the command

singularity exec /software/singularity/containers/PacBioSuite-7.0.0.63985-1.centos7.simg bax2bam data/00$NUM.1.bax.h5 data/00$NUM.2.bax.h5 data/00$NUM.3.bax.h5 -o 00$NUM –subread