Linux.conf.au 2018 – Day 5 – Keynote – Jess Frazelle

Keynote: Containers aka crazy user space fun

  • Work at Microsoft on Open Source and containers, specifically on kubernetes
  • Containers vs Zones vs Jails vs VMs
  • Containers are not a first class concept in the kernel.
    • Namespaces
    • Cgroups
    • AppArmour in LSM (prevent mounting, writing to /proc etc) (or SELinux)
    • Seccomp (syscall filters, which allowed or denied) – Prevent 150 other syscalls which are uncommon or dangerous.
      • Got list from testing all of dockerhub
      • eg CLONE, UNSHARE
      • NoNewPrivs (exposed as “AllowPrivilegeEsculation” in K8s)
      • rkt and systemd-nspawn don’t 100% follow
  • Intel Clear containers are really VMs

History of Containers

  • OpenVZ – released 2005
  • Linux-Vserver (2008)
  • LXC ( 2008)
  • Docker ( 2013)
    • Initially used LXC as a backend
    • Switched to libcontainer in v0.7
  • lmctfy (2013)
    • By Google
  • rkt (2014)
  • runc (2015)
    • Part of Open container Initiative
  • Container runtimes are like the new Javascript frameworks

Are Containers Secure

  • Yes
  • and I can prove it
  • VMs / Zones and Jails are like all the Lego pieces are already glued togeather
  • Containers you have the parts seperate
    • You can turn on and off certain namespaces
    • You can share namespaces between containers
    • Every container in k8s shares PID and NET namespaces
    • Docker has sane defaults
    • You can sandbox apps every further though
  • https://contained.af/
    • No one has managed to break out of the container
    • Has a very strict seccomp profile applied
    • You’d be better off attacking the app, but you are still running a containers default seccomp filters

Containerizing the Desktop

  • Switched to runc from docker (had to convert stuff)
  • rootless containers
  • Runc hook “netns” to do networking
  • Sandboxed desktop apps, running in containers
  • Switch from Debian to CoreOS Container Linux as base OS
    • Verify the integrity of the OS
    • Just had to add graphics drivers
    • Based on gentoo, emerge all the way down

What if we applied the the same defaults to programming languages?

  • Generate seccomp filters at build-time
    • Previously tried at run time, doesn’t work that well, something always missed
    • At build time we can ensure all code is included in the filter
    • The go compiler writes the assembly for all the syscalls, you can hijack and grab the list of these, create a seccomp filter
    • No quite that simply
      • plugins
      • exec external stuff
      • can directly exec a syscall in go code, the name passed in via arguments at runtime
  • metaparticle.io
    • Library for cloud-native applications

Linux Containers in secure enclaves (SCONE)

  • Currently Slow
  • Lots of tradeoffs or what executes where (trusted area or untrsuted area)

Soft multi-tenancy

  • Reduced threat model, users not actively malicious
  • Hard Multi-tenancy would have potentially malicious containers running next to others
  • Host OS – eg CoreOs
  • Container Runtime – Look at glasshouse VMs
  • Network – Lots to do, default deny in k8s is a good start
  • DNS – Needs to be namespaced properly or turned off. option: kube-dns as a sidecar
  • Authentication and Authorisation – rbac
  • Isolation of master and System nodes from nodes running containers
  • Restricting access to host resources (k8s hostpath for volumes, pod security policy)
  • making sure everything else is “very dumb” to it’s surroundings

 

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Linux.conf.au 2018 – Day 4 – Session 3

Insights – solving every problem for good Paul Wayper

Sysadmins

  • Too much to check, too little time
  • What does this message mean again
  • Too reactive

How Sysadmins fix problems

  • Read text files and command output
  • Look at them for information
  • Check this information against the knowlede
  • Decide on appobiate solution

Insites

  • Reads test files and outputs
  • Process them into information
  • Use information in rules
  • Rules provide information about Solution

Examples

  • Simple rule – check “localhost” is in /etc/hosts
  • Rule 2 – chronyd refuses to fix server’s time since is out by more than 1000s
    • Checks /var/log/message for error message from chrony
  • Insites rolls up all the checks against messages, so only down once
  • Rule 3 – rsyslog dropping messages

Website

http://red.ht/demo_rules

 

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Linux.conf.au 2018 – Day 4 – Session 2

Personalisation at Scale: A “Cookie Cutter” Approach Jim O’Halloran

  • Impact on site performance on conversion is huge
  • Magento
    • LAMP stack + Redis or memcached
    • Generally App is CPI bound
    • Routing / Rendering still time consuming
  • Varnish full page caching (FPC)
  • But what about personalised content?
  • Edge Side Includes (ESIs)
    • But ESIs run in series, is slllow when you have many
    • Content is nont cacheable, expensive to calculate, significant render time
    • ESI therefore undermines much advantage of FPC
  • Ajax
    • Make ajax request and fetch personalised content
    • Still load on backend
    • ESI limitations plus added network latency
  • Cookie Cutter
    • When an event occurs that modifies personalisation state, send a cookies containing the required data with the response.
    • In the browser, use the content of that cookie to update the page

Example

  • Goto www.example.com
    • Probably cached in varnish
    • I don’t have a cookie
    • If I login, uncachable request, I am changing login state
    • Response includes Set-Cookie header creating a personalised cookie
  • Advantages
    • No backend requests
    • Page data served is cached always
  • How big can cookies be?
    • RFC 6265 has limits but in reality
    • Actual limit ~4096 bytes per cookie
    • Some older browsers also limit to ~4096 bytes total per domain

Potential issues

  • Request Size
    • Keep cookies small
      • Store small values only, No pre-rendered markup, No larger data structures
    • Serve static assets via CDN
    • Lot of stuff in cart can get huge
  • Information leakage
    • Final URLs leaked to unlogged in users
  • Large Scale changes
    • Page needs to look completely different to different users
    • Vary headers might be an option
  • Formkeys
    • XSRF protection workarounds
  • What about cache misses
    • Megento assembles all it’s pages from a series of blocks
    • Most parts of page are relatively static (block cache)
    • Aligent_CacheObserver – Megento extension that adds cache tags to blocks that should be cached but were not picked up as cachable by default
    • Aoe_TemplateHints – Visibility into Block cache
    • Cacheing != Performance Optimisation – Aoe_Profiler

Availability

  • Plugin availbale for Megento 1
    • Varnish CookieCutter
  • For Magento 2 has native varnish
    • But has limitations
    • Maybe some off CookieCutter stuff could improve

Future

  • localStorage instead of cookies


 

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Linux.conf.au 2018 – Day 4 – Session 1

Panel: Meltdown, Spectre, and the free-software community Jonathan Corbet, Andrew ‘bunnie’ Huang, Benno Rice, Jess Frazelle, Katie McLaughlin, Kees Cook

  • FreeBSD only heard 11 days beforehand. Would have liked more notice
  • Got people involved from the Kernel Summit in Oct
  • Hosting company only heard once it went official, been busy patching since
  • Likely to be class-action lawsuit for $billions. That might make chip makers more paranoid about documentation and disclosure.
  • Thoughts in embargo
    • People noticed strange patches going in beforehand.
    • Only broke 6 days early, had been going for 6 months
    • “Linus is happy with this, something is terribly wrong”
    • Sad that the 2nd-tier cloud providers didn’t know. Exclusive club and lines as to who got informed were not clear
    • Projects that don’t have explicit relationship with Intel didn’t get informed
  • Thoughts on other vendors
    • This class of bugs could affect anybody, open hardware would probably not fix
    • More open hardware could enable people to review the processors and find these from the design rather than poking around
    • Hard to guarantee the shipped hardware matches the design
    • Software people can build everything at home and check. FABs don’t work at home.
  • Speculative execution warned about years ago. Danger ignored. How to make sure the next one isn’t ignored?
    • We always have to do some risky stuff
    • The research on this built up slowly over the years
    • Even if you have only found impractical attacks against something doesn’t mean the practical one doesn’t exist.
  • What criteria do we use to decide who is in?
    • Mechanisms do exist, they were mainly not used. Perhaps because they were for software vulnerabilities
  • Did people move providers?
    • No but Containers made things easier to reboot stuff and shuffle
  • Are there similar vulnerabilities ( similar or general hardware ) coming along?
    • The Kernel page-table patches were fairly general, should cover many similar ones
    • All these performance optimising bit of your CPU are now attack surfaces
    • What are people going to do if this slows down hardware too much?
  • How do we explain problems like these to politicians etc
    • Legos
    • We still have kernel devs getting their laptops
  • Can be use CPUs that don’t have speculative execution?
    • Not really. Back to 486s
  • Who are we protesting against with the embargo?
    • Everybody
    • The longer period let better fixes get in
    • The meltdown fix could be done in semi-public so had better quality

What is the most common street name in Australia? Rachel Bunder

  • Why?
    • Saw a map with most common name by US street
  • Just looking at name, not end bit “park” , “road”
  • Data
    • PSMA Geocoded national address file – Great but came out after project
    • Use Open Street Maps
  • Started with Common Name in Sydney
    • Used Metro Extracts – site closing down soon
    • Format is geojson
    • Road files separately provided
  • Procedure
    • Used python, R also has good features and libaraies
    • geopandas
    • Had some paths with no names
    • What is a road? – “Something with a name I can drive a car on”
  • Sydney
    • Full street name
      • Victoria Road
      • Pacific Highway
      • oops like like names are being counted twice
    • Tried merging them together
    • Roads don’t 100% match ends. Added function to fuzzy merge the roads that are 100m apart
    • Still some weird ones but probably won’t affect top
    • Second attempt
      • Short st, George st, William st, John st, Church st
  • Now with just the “name bit”
    • Tried taking out just the last name. ended up with “the” as most common.
    • Started with “The” = whole name
    • Single word = whole name
    • name – descriptor – suffex
    • lots of weird names
    • name list – Park, Victoria, Railway, William, Short
  • Wouldn’t work in many other counties
  • Now for all over Australia
    • overpass data
    • Downloaded in 50kmx50x squares
  • Lessons
    • Start small
    • Choose something familiar
    • Check you bias (different naming conventions)
    • Constance vigerlence
    • Know your problem
  • Common plant names
    • Wattle – 15th – 385
  • Other name
    • “The Esplanade” more common than “The Avenue”
  • Top names
    • 5th – Victoria
    • 4th – Church – 497
    • 3rd – George –  551
    • 2nd – Railway
    • 1st – Park – 693
  • By State
    • WA – Forest
    • SA – Railway
    • Vic – Park
    • Tas – Esplanade
    • NT – Smith/Stuart
    • NSW – Park

 

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Linux.conf.au 2018 – Day 4 – Keynote – Hugh Blemings

Wandering through the Commons

Reflections on Free and Open Source Software/Hardware in Australia, New Zealand and beyond

  • Past Linux.conf.au’s reviewed
  • FOSS in Aus and NZ
    • Above per capita
  • List of Aus / NZ people and their contributions
    • John Lions , Lions book on Unix
    • Pia Andrews/Waugh/Smith – Open Government, GovHack, Linux Australia, Open Data
    • Vik Oliver – 3D Printing
    • Clare Cuuran – Open Government in NZ
    • plus a bunch of others

Working in Free Software and Open Hardware

  • The basics
    • Be visable in projects of relevance
      • You will be typed into Google, looked at in GitHub
    • Be yourself
      • But be business Friendly
    • Linkedin is a thing, really
    • Need a accurate basic presence
  • Finding a new job
    • Networks
    • Local user groups
    • Conferences
    • The projects you work on
  • Application and negotiation
    • Be professional, courteous
    • Do homework about company and culture
    • Talk to people that work there
    • Spend time on interview prep
      • Know your stuff, if you don’t know, say so
    • Think about Salary expectations and stick to them
      • Val Aurora’s page on this is excellent
    • Ask to keep copyright on your code
      • Should be a no-brainer for a FOSS.OH company
  • In the Job
    • Takes time to get into groove, don’t sweat it
    • Get out every now and then, particularly if working from home
    • Work/life balance
    • Know when to jump
      • Poisonous workplaces
    • An aside to People’s managers
      • Bring your best or don’t be a people manager
      • Take your reports welfare seriously

Looking after You

  • Ours is in the main a sedentary and solitary pursuit
    • exercise
  • Sitting and standing in front of a desk all day is bad
    • takes breaks
  • Depression is a real thing
  • Eat more vegetables
  • Find friends/colleagues to exercise with

Working if FOSS / OH – Staying Current

  • Look over a colleagues shoulder
  • Do something that is not part of your regular job
    • low level programming
    • Karger systems, Openstack
  • Stay uptodate with Security Blogs and the like
    • Many of the attack vectors have generic relevance
  • Take the lid off, tinker with hardware
    • Lots of videos online to help or just watch

Make Hay while the Sun Shines

  • Save some money for rainy day
  • Keep networks Open
  • Even when you have a job

You’re fired … Now What? – In a moment

  • Don’t panic
    • Going out in a twitter storm won’t help anyone
  • It’s not personal
    • It is the position that is no longer needed, not you
  • If you think it an unfair dismissal, seek legal advice before signing anything
  • It is normal to feel rubbish
  • Beware of imposter syndrome
  • Try to keep 2-3 opportunities in the pipeline
  • Don’t assume people will remember you
    • It’s not personal, everyone gets busy
    • It’s okay to (politely naturally) follow up periodically
  • Keep search a little narrow for the first week or two
    • The expand widely
  • Balance take “something/everything” as better than waiting for your dream job

Dream Job

  • Power 9 CPU
    • 14nm process
    • 4GHz, 24 cores
    • 25km of wires
    • 8 billion transisters
    • 3900 official chips pins
    • ~19,000 connections from die to the pin

Conclusions

  • Part of a vibrant FOSS/OH community both hear and abroad
  • We have accomplished much
  • The most exciting (in both senses) things lie before us
  • We need all of you to be part at every level of the stack
  • Look forward to working with you…
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Linux.conf.au 2018 – Day 3 – Session 3 – Booting

Securing the Linux boot process Matthew Garrett

  • Without boot security there is no other security
  • MBR Attacks – previously common, still work sometimes
  • Bootloader attacks – Seen in the wild
  • Malicious initrd attacks
    • RAM disk, does stuff like decrypt hard drive
    • Attack captures disk pass-shrase when typed in
  • How do we fix these?
    • UEFI Secure boot
    • Microsoft required in machines shipped after mid-2012
    • sign objects, firmware trusts some certs, boots things correctly signed
    • Problem solved! Nope
    • initrds are not signed
  • initrds
    • contain local changes
    • do a lot of security stuff
  • TPMs
    • devices on system motherboards
    • slow but inexpensive
    • Not under control of the CPU
    • Set of registers “platform configuration registers”, list of hashes of objects booted in boot process. Measurements
    • PCR can enforce things, stop boots if stuff doesn’t match
    • But stuff changes all the time, eg update firmware . Can brick machine
  • Microsoft to the resuce
    • Tie Secure boot into measured boot
    • Measure signing keys rather than the actual files themselves
    • But initrds are not signed
  • Systemd to the resuce
    • systemd boot stub (not the systemd boot loader)
    • Embed initrd and the kernel into a single image with a single signature
    • But initrds contain local information
    • End users should not be signing stuff
  • Kernel can be handed multiple initranfs images (via cpio)
    • each unpacked in turn
    • Each will over-write the previous one
    • configuration can over-written but the signed image, perhaps safely so that if config is changed, stuff fails
    • unpack config first, code second
  • Kernel command line is also security sensative
    • eg turn off iommu and dump RAM to extract keys
    • Have a secure command line turning on all security features, append on the what user sends
  • Proof of device state
    • Can show you are number after boot based on TPM. Can compare to 2FA device to make sure it is securely booted. Safe to type in passwords
  • Secure Provision of secrets
    • Know a remote machine is booted safely and not been subverted before sending it secret stuff.
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Linux.conf.au 2018 – Day 3 – Session 2

Dealing with Contributor Overload Holden Karau

  • Developer Advocate at Google
  • Apache Spark, Contributor to BEAM

Some people from big projects, some from projects hoping to get big

  • Remember it’s okay to not fix it all
  • The fun of a small project
    • Simple communication
    • Aligned incentives
    • Easy to tell who knows what
    • Tight community
  • The fun of a parge project
    • More people to do the work
    • More impact and people thanking you
    • Lots of ideas and experiences
    • If $s then fun conferences
    • Get paid to work on it.
  • Is my project on Fire? or just lots of people on it.
    • Measurable
      • User questions spike
      • issue spike
    • Lesss measurable
      • Non-explicit stuff not being passed on
  • Classic Pipeline
    • Users -> contributors -> committers _> PMC
    • Each stage takes times
    • Very leaky pipeline, perhaps it leaks too much
  • With hyper-growth project can quickly go south
    • Committer:user ration can’t get too far out.
  • Even without hyper-growth: sadness
    • Same thing happens, but slower
  • Overload – Mitigation
    • You don’t have to answer everyone, this can be hard
    • Stackoverflow
    • Are your answers easily searchable
    • Knowledge base – “do you mean”
    • Take time and look for patterns in questions
    • Find people who like writing and get to to write a book
      • Don’t to for core committers, they will have no time for anything else
  • Issue overload
    • Try and get rid of duplicate tickets
    • Autoclose tickets – mixed results
  • How to deal with a spike
    • Raise the bar
    • Make it easier
    • Get Perl to solve the problem
  • Raising the bar
    • Reject trivial changes – reduces the onramp
    • Add weird system – more posts on how to contribute
  • What can Perl solve
    • Style guide
    • bot bot bots
    • make it faster to merge
    • Improve PR + reviewer notice
    • Can increase productivity
  • Add more committers
    • Takes time and effort
    • People can be shy
    • Make a guide for new folks to follow
    • Have a safe space for people to ask questions
  • Reduce overhead for contributing well
    • Have doc on how to contribute next to the code, not elsewhere that people have to search for.

The Open Sourcing of Infrastructure Elizabeth K. Joseph

The recent history of infrastructure

  • 1998
    • To make a server use Solaris or NT. But off a shelf
    • Linux seen as Cheap Unix
    • Lots of FUD

Got a Junior Sysadmin Job

  • 2004
    • Had to tell people the basics “What is free software?”  , “Using Open Source Web Applications to Produce Business Results”
    • Turning point LAMP stack
    • Flood of changes on how customers interacted with software over last
      • Reluctance to be locked-in by a vendor
      • Concerns of security
      • Ability to fix bugs ourselves
      • Innovation stifled when software developed in isloation

Last 10 years

  • Changes in how peopel interacted with software
    • Downtime un-acceptable
    • Reliance of scaling and automation
    • Servers as Pets -> cattle
    • Large focus on data

Open Source is now Ubiquitous

  • Even Microsoft is using it a lot and interacting with the community

Operations tools were not as Open Sourced

  • Configuration Management
    • puppet modules, chef playbooks
  • Open application definitions – juhu charms, DC?OS Universe Catalog
  • Full disk images
    • Dockerhub

The Cloud

  • Cloud is the new propriatory
  • EC2-only infrastructure
  • Questions you should ask beforehand
    • Is your service adhering to open standards or am I locked in?
    • Recourse if the company goes out of business
    • Does vendor have a history of communicating about downtime and security problems?
    • Does vendor responds to bugs and feature requests?
    • Will the vendor use data in a way I’m not comfortable with?
    • Initial costs may be low, but do you have a plan to handle long term, growing costs
  • Alternatives
    • Openstack, Kubernetes, Docker Swarm, DC/OS with Apache Mesos

Hybrid Cloud

  • Tooling can be platform agnostic
  • Hard but can be done
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Linux.conf.au 2018 – Day 3 – Session 1 – k8s @ home and bad buses

How to run Kubernetes on your spare hardware at home, and save the world Angus Lees

  • Mainframe ->
  • PC ->
  • Rackmount PC
    • Back the rackmount PC even with built-in redundancy will still fail. Or the location will go offline, or your data spreads across multiple machines
  • Since you need to have distributed/redundancy anyway. New model (2005). Grid computing. Clever software, dumb hardware. Loosely coupled servers
    • Libraries > RPC / Microservices
    • Threadpool -> hadoop
    • SQL -> key/store
    • NFS -> Object store
    • In-place upgrades -> “Immutable” image-based build from scratch
  • Computers in clouds
    • No cases. No redundant Power, journaling on filesystems turned off, etc
  • Everything is in clouds – Secondary effects
    • Corperate driven
    • Apache license over GPL
    • Centralised services rather than federated protocols
    • Profit-driven rather than scrating itches
  • Summary
    • Problem
      • Distributed Systems hard to configure
      • Solutions scale down poorly
      • Most homes don’t have racks of servers
    • Implication
      • Home Free Software “stuck” at single-machine architecture
  • Kubernetes (lots of stuff, but I use it already so just doing unique bits)
    • “Unix Process as a service”
    • Inverts the stack. Data is important then app. Kernel and Hardware unimportant.
    • Easy upgrades, everything is an upgrade
    • Declarative API , command line interface
  • “We’ve conducted this experiment for decades now, and I have news for you, Hardware fails”

Hardware at Home

  • Raid used to be “enterprise” now normal for home
  • Elastic compute for home too
  • Kubernetes for Home
    • Budget $100
      • ARM master nodes
      • Mixed architecture
    • Assume single layer-2 home ethernet
    • Worker nodes – old $500 laptops
      • x86-64
      • CoreOS
      • Broken screens, dead batteries
    • 3 * $30 Banana pis
      • Raspberry Pi2
      • armv7a
      • containOS
    • Persistentvolumes
      • NFS mount from RAID server
    • Service – keepalived-vip
    • Ingress
      • keepalived and nginx-ingress , letsEncrypt
      • Wildcard DNS
    • Status
      • Works!
      • Printing works
      • Install: PXE boot and run coreos-install
    • Status – ungood
      • Banana PIs a bit too slow.
    • github.com/anguslees/k8s-home

Is the 370 the worst bus route in Sydney? Katie Bell

  • The 370 bus
    • Goes UNSW and Sydney University. Goes around the city
  • If bus runs every 15 minutes, you should not be able to see 3 at once
  • Newspaper articles and Facebook group about how bad it is.
  • Two Questions
    • Bus privitisation better or worse
    • Is the 370 really the worst
  • Data provided
    • Lots of stuff but nothing the reliability
    • But they do have realtime data eg for the Tripetime app (done via a 3rd party)
    • They have a API and Key with standard format via GTFS
  • But they only publish “realtime” data, not the old data
    • So collected the realtime data, once a minute for 4 months
    • 557 GB
  • Format
    • zipfile of csv files
    • IDs sometimes ephemeral
    • Had to match timetable data and realtime data
    • Data had to be tidied up – lots
  • Processing realtime data
    • Download 1 minute
    • Parse
    • Match each of around ~7000 trips in timetable (across all of NSW)
    • Write ~20000 realtime updates to the DB
    • Running 5 EC2 instances at leak
    • Writing up to 40MB/s to the DB
  • Is the 370 the worst?
    • Define “worst”
    • Found NSW definition of what an on-time bus is.
    • Now more than 5:59 late or 1:59 early. Measured start/middle/end
    • Victoria definition strictor
    • She defined:
      • Early: more than 2min early
      • On time: 2m early – 5 min late
      • late more than 5m late
      • Very late – more thna 20m late
    • Across all trips
      • 3.7 million trips
      • On time 31%
      • More than 20m late 2.86%
    • Best routes
      • Nightime buses
      • Outside of Sydney
      • Shorter routes
      • 86% – 97% or better
    • Worst
      • Less than 5% on time
      • Longer routes
      • 370 is the 22nd worst
        • 8.79% on time
    • Worst routes ( percent > 20 min late)
      • 23% of 370 trips (6th worst)
      • Lots of Wollongong
    • Worst agencies
      • No obvious difference between agencies and private companies
    • Conclusion
      • Privatisation could go either way
      • 370 is close to the worst (277 could be worse) in Sydney
    • bus-shaming.com
    • github.com/katharosada/bus-shaming

Questions

  • Used Spot instances to keep cost down
  • $200 month on AWS
  • Buses better/worse according to time? Now checked yet
  • Wanted to calculate the “wait time” , not done yet.
  • Another feed of bus locations and some other data out there too.
  • Lots of other questions
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Linux.conf.au 2018 – Day 3 – Keynote – Karen Sandler

Executive director of Software Freedom Conservancy

Previously spoke that LCA 2012 about closed-source software on her heart implant. Since then has pivoted career to more open-source advocacy in career.

  • DMCA exemption for medical device research
  • When you ask your doctor about safety of devices you sound like a conspiracy theorist
  • Various problems have been highlighted, some progress
  • Some companies addressing them

Initially published paper highlighting problem without saying she had the device

  • Got pushback from groups who thought she was scaremongering
  • Companies thinking about liability issues
  • After told story in 2012 things improved

Had to get new device recently.

  • Needed this disabled since her jobs pisses off hackers sometimes
  • All manufacturers said they could not disable wireless access
  • Finally found a single model that could be disabled made by a European manufacturer

 

Note: This is a quick summary, Lots more covered but hard to cover. Video should be good. Her slides were broken though much of the talk be she still delivered great talk.

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Linux.conf.au 2018 – Day 2 – Keynote – Matthew Todd

Collaborating with Everybody: Open Source Drug Discovery

  • Term used is a bit undefined. Open Source, Free Drugs?
  • First Open Source Project – Praziquantel
    • Molecule has 2 mirror image forms. One does the job, other tastes awful. Pills were previously a mix
    • Project to just have pill with the single form
      • Created discussion
      • Online Lab Notebook
      • 75% of contributions were from private sector (especially Syncom)
      • Ended up finding a approach that worked, different from what was originally proposed from feedback.
      • Similar method found by private company that was also doing the work
  • Conventional Drug discovery
    • Find drug that kills something bad – Hit
    • Test it and see if it is suitable – Led
    • 13,500 molecules in public domain that kill maleria parasite
  • 6 Laws of Open Scrience
    • All data is open and all ideas are shared
    • Anyone can take part at any level of the project
  • Openness increasing seen as a key
  • Open Source Maleria
    • 4 campaigns
    • Work on a molecule, park it when doesn’t seem promising
    • But all data is still public
  • What it actually is
    • Electronic lab book (80% of scientists still use paper)
    • Using Labtrove, changing to labarchives
    • Everything you do goes up every day
    • Todo list
      • Tried stuff, ended up using issue list on github
      • Not using most other github stuff
    • Data on a Google Sheet
    • Light Website, twitter feed
  • Lab vs Code
  • Have a promising molecule – works well in mice
    • Would probably be a patentable state
    • Not sure yet exactly how it works
  • Competition – Predictive model
    • Lots of solutions submitted, not good enough to use
    • Hopeful a model will be created
  • Tried a a known-working molecule from elsewhere, but couldn’t get it to work
    • This is out in the open. Lots of discussion
  • School group able to recreate Daraprim, a high-priced US drug
  • Public Domain science is now accepted for publications
  • Need to to make computers understand molecule digram and convert to representative format which can then be search one.
  • Missing
    • Automated links to databases in tickets
    • Basic web page stuff, auto-porting of data, newsletter, become non-profit, stickers
    • Stuff is not folded back into the Wiki
  • OS Mycetoma – New Project
    • Fungus with no treatment
    • Working on possible molecule to treat
  • Some ideas on how to get products created this way to market – eg “data exclusivity”

 

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