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Spencer Bliven
Bioinformatics PhD student at UCSD
Bioinformatics PhD student at UCSD

Spencer's posts

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I got some really cool models that were created from medical imaging data. Unfortunately they have lots of "foam" due to the thresholding algorithm used to create the original mesh. I've been trying to clean this up in blender (see linked thread), but it is very slow and tedious. Does anyone have suggestions for how to smooth this down, remove any "bridges" coming out from the main surface, and get it into a suitable state for printing? I'm looking for free mac/linux/online tools.

I've never really solved oozing issues with my makergear hotend. I get lots of threading, slightly rough vertical walls, terrible bridges, and other signs of oozing. I've tried changing temperature, tweaking retraction, changing speeds, etc.

I've tweaked things enough that I'm considering hardware upgrades. I'm currently printing with 3mm PLA through a .5mm nozzle. Would switching to 1.75mm filament and a .35-.4mm nozzle be likely to improve print quality by reducing the reservoir volume and increasing extrusion volume accuracy?

Anyone know a european source of straight 3mm filament, suitable for use in a 3Doodler? I've read that trying to straighten out spooled filament doesn't work well, but the official price is ~$200/kg.

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Congratulations to the BioJava team ( +Andreas Prlic +Spencer Bliven and many others ) on their latest release BioJava 4.0.

New Features:

• Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations. (many contributors, including @benjamintboyle and @josemduarte)
• Improved handling of exceptions (@dmyersturnbull)
• Removed deprecated methods
• Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and @sbliven)
• Updated dependencies where applicable
• Available on Maven Central (@andreasprlic and @heuermh)

Improved Genbank parser, including support for feature records, qualifiers, and nested locations. (@paolopavan and @jgrzebyta)

• Better support for crystallographic information, including crystallographic operators, unit cells, and protein-protein interfaces. (@josemduarte)
• Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven)
Better command-line tools for structure alignment (@sbliven)
• New algorithm for symmetry detection in biological assemblies (@pwrose)
• New algorithm for fast contact calculation, both intra-chain and inter-chain (@josemduarte)
• Support for Accessible Surface Area (ASA) calculation through and implementation of the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) (@josemduarte)
• Support for large structures (memory permitting) and multi-character chain IDs.
• Default to mmCIF file format, as recommended by the wwPDB

This version is compatible with Java 6, 7, and 8.

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The Personal Genome Project is looking for San Diego volunteers to be sequenced. I would totally participate if I were in town.

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Wow, a nematode wirehead, living in a virtual world. We feed it false sensory data and let the worm drive its robot body around.
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