12 must know Zotero tips and techniques

http://ideophone.org/12-zotero-tips-and-techniques/

Posted on November 30, 2008

Zotero is getting better and better. In a while, version 1.5 will bring synchronization, online backup of your library, +1100 CSL citation styles, and PDF metadata extraction (for the daring, a sync preview version is available). But even in its current incarnation Zotero is easily one of the best bibliographic managers out there. Here are twelve tips and tricks that help you to get the most out of it.

1. Drag files from the web right into your library
   Got a reference in your library, but no PDF? Or saved an item from a repository which doesn’t provide a fulltext version? Do a quick search for the title on Google Scholar — it is good at finding PDFs on author’s webpages. If you find one, just drag the link from the page onto the reference in your library. Zotero stores and attaches the PDF for you.
2. Enter a series of items by duplicating a template
   Adding a series of related references to your library? Start with one item for which you fill in the fields that are the same for all items (e.g. editors, book title, year, publisher, place) and duplicate it (Right-click > Duplicate item). Then fill in the particularities.
3. Quick Copy a citation using Ctrl+Alt+C or drag and drop
   Sending a PDF to a colleague, or mentioning a reference somewhere? Quickly copy the citation by selecting the reference and pressing Ctrl+Alt+C (Command+Alt+C on the Mac), or simply drag it from Zotero onto any edit window (for example a new email). The default output style can be specified under Preferences > Export; the shortcut key can be customized under Shortcut keys.
4. Have Zotero index your PDFs
   Zotero can index your PDF attachments and make them fully searchable, turning your library from a mere linked catalogue into a Google Books of sorts. The option is turned off by default because it relies on an external open source program (pdf2txt) which is not distributed with Zotero. However, Zotero can automatically install it and enable fulltext indexing: simply go to Preferences > Search and click on the ‘Check for installer’ button. For more info see pdf fulltext indexing in the Zotero documentation.
5. Start quicksearch with ” to trigger advanced search
   By default, Zotero starts searching when you put the first few characters in the Search box. In a large library with fulltext indexing enabled, this can be tiresome (you wanted to look for “statistical methods”, but Zotero locks down searching for “st”). To avoid this, simply start your search with ” (double quote) to have Zotero wait until you finish typing and hit enter.
6. Press Ctrl to find out in which collections an item is
   Looking at an item in your library and wondering whether you already categorized it? Press Control and Zotero will highlight the collections in which it is contained.
7. Relocate your Zotero folder to a more sensible place
   The default place for the Zotero database and attachments in right in your Firefox profile, which isn’t the easiest to locate whichever OS you are on. Go to Preferences > Advanced to customize the storage location. You can place it in a folder that is included in your regular backup schedule or put it on a portable drive so that your library always travels with you (tip: combine it with Firefox Portable, which you can even use without administrator rights).
8. Keep track of recent additions using a saved search
   Often you add new items without worrying about tagging or putting them in collections. Click Advanced search, select “Dated Added” > “is in the last” > X “days/months” and fill in the desired period; then save the search. This gives you a dynamically updated overview of your latest additions, so that you can go back to them and do the categorization and tagging work when it suits you.
9. Tag multiple items at once
   Want to tag multiple items at once? Select them, make sure the tag selector is visible in the left pane, and drag them onto the tag you want to use. The tag will be applied to all items.
10. Tag incomplete items to find them back and fix them later
    Sometimes you know an item has incomplete metadata (e.g. missing page numbers or publisher), but you don’t have the time to fix it right away. Make it a habit to tag such items (“needs metadata”) when you see them. Now you can find them and fix them whenever you have some time to kill.
11. Use a separate folder for files to be ingested
    Someone gives you a bunch of PDFs to read; or you download a paper somewhere without having the metadata handy. Make it a habit to save such files in a subfolder /new/ in your Zotero folder. Then once in a while go through that folder. Do a quick search for the title on your favourite repository, grab the metadata, and then drag the PDF from your filemanager onto the reference in Zotero. Much better than having those loose PDFs scattered all over your hard drive (or in your mailbox!) — and it helps you keep track of your reading history too.
12. Display a timeline to visualize your bibliography
    Not a feature you’ll use everyday, but a neat one nonetheless: Zotero can display your library, or portions of it, on a timeline. Select a group of references, a tag, or a collection and click ‘Create timeline’ (in the Gear menu). This gives you an overview of the items in time. Now you have to ask yourself: is the recency bias due to your reading habits or is it really true that most of the research was done in the last twenty years? (Probably a bit of both.)

OneNote 2010 on Live.com - 工作、任務、研究

OneNote 2010 on Live.com - 工作、任務、研究

Luteolin is a potent inhibitor for AGE formation

Wu, C. H., & Yen, G. C. (2005). Inhibitory effect of naturally occurring flavonoids on the formation of advanced glycation endproducts. J Agric Food Chem, 53, 3167-3173.

PubMed Central

今天發現NCBI裡面的下拉選單裡有一個PMC，是PubMed Central的縮寫，裡面查到的papers都直接有PDF下載的連結，應該是PubMed精選過的papers，像今天查到的Automics軟體的介紹總共有101篇，但收納入PMC的就只有一篇：

代表如果沒有時間的話，就唸PMC裡面的paper就可以了。

另外，如果想限制查到的paper只要有免費的才列出，也有選項可以設定：

美國國家資訊中心的服務真是貼心啊！

DEAE (Diethylaminoethyl) Cellulose (More fun with starch)

DEAE (Diethylaminoethyl) Cellulose (More fun with starch)
30th May 2006

[Data source: http://www.moleculeoftheday.com/]

You have probably heard of chromatography. This is a chemical technique for separating mixtures of compounds. Various “stationary phases

You have probably heard of chromatography. This is a chemical technique for separating mixtures of compounds. Various “stationary phases” can be used to separate compounds based on different characteristics. Probably the most common is silica, which is just pure, clean sand (speaking a little loosely. It’s so pure you wouldn’t recognize it as sand. It’s a fine white powder and very homogeneous in size.) It separates compounds based on their polarity. It is the most common medium used by organic chemists because it’s relatively cheap and it works on a wide variety of substrates.

Biochemistry makes it trickier. First of all, everything’s dissolved in water, which is the most polar solvent most people will ever encounter. Silica chromatography with water just doesn’t work. It’s done with organic solvents like ethyl acetate and methylene chloride. Biomolecules, as a rule, don’t take well to being dissolved in anything but water. A lot of the time (especially with proteins), you’re worried about a specific three-dimensional structure. Organic molecules, as a rule, don’t really care. This is largely because most of them are too small to have enough freedom to fold into anything interesting. This is why I can show the daily molecule as a stick drawing and not have to worry about 3D structure.

Because of this, biochemists are forced to use different stationary phases/resins instead of silica. One common one is DEAE cellulose (diethylaminoethyl cellulose):

As you can imagine, it’s made from cellulose, largely because the stuff is so cheap. The business end is that diethylaminoethyl moiety. In water, at any pH below the pKa of 11.5 (just about any pH you would ever use; biologists usually work between pH ~5 and ~8, 7 being “neutral”, less being acidic, more being basic), it is predominantly in that form on the right. It is positively charged and pretty good at binding anions (negatively charged species) to its surface. You can take hundreds of milliliters of solution containing less than a milligram of your favorite anion, and flow it over a few mL of the resin (it is present as sort of a slurry - almost exactly like oobleck.) Almost all your anion will stick to the resin. It can then be eluted (washed off) with a buffer with a lot of salt.

Let’s say we’re using sodium chloride and we’re purifying DNA. Initially, when we load the column with the DNA, it should be dissolved in a low-salt buffer (preferably a buffer like tris rather than phosphate, since phosphate is itself an anion and will stick to the column, competing with our DNA). We can wash the column repeatedly with low-salt buffer (say, 100mM) and very little DNA will come off, but that which doesn’t stick will. If we start washing high-salt buffer over it (say, 2M), the chloride ions will start competing with the DNA for binding those positively charged diethylammoniumethyl moieties, and the DNA will wash off the column.

The principle works similarly for proteins, but you will undoubtedly use different concentrations of salt - DEAE works especially well for DNA because DNA has so much more negative charge than anything else. That 100mM salt would probably elute many proteins, which is great; we’re left with only DNA.

That one might have been a little more in depth than usual, sorry if I lost you. Night.

化學軟件

化學軟件
作者: xiongguangwei 發佈日期: 2007-3-14 查看數: 248 出自: http://emuch.net


分子模型化
3D分子圖形顯示工具 (RasMol and OpenRasMol)(免費)
AMBER (分子力學力場模擬程序)
autodock (分子對接軟件)(免費)
GROMACS (分子動力學軟件)(免費)
GULP (General Utility Lattice Program)(免費)
NIH分子模擬中心的化學軟件資源導航(Research Tools on the Web)
X-PLOR (大分子X光晶體衍射、核磁共振NMR的3D結構解析)(免費)
高通量篩選軟件PowerMV (統計分析、分子顯示、相似性搜索等)(免費)
化合物活性預測程序PASS(部分免費)
計算材料科學Mathub

C4：Cabrillo學院化學可視化項目以及相關軟件(免費)
Databases and Tools for 3-D Protein Structure Comparison and Alignment (三維蛋白質結構對比)(免費)
Democritus (分子動力學原理演示軟件)
DPD應用軟件cerius2(免費)
EMSL Computational Results DataBase (CRDB)
MARVIN'S PROGRAM (表面與界面模擬)(免費)
XLOGP(計算有機小分子的脂水分配係數)(免費)
量子化學軟件中文網
美國斯克利普斯研究院：金屬蛋白質結構和設計項目(免費)
http://folding.stanford.edu/(免費)

3D Molecular Designs (蛋白質及其他3D分子物理模型快速成型技術)
3D-Dock Suite Incorporating FTDock, RPScore and MultiDock (3D分子對接)(免費)
AMSOL (半經驗量子化學計算)(免費)
Amsterdam Density Functional (ADF, 第一原理電子結構計算)
Bilbao晶體學服務器(免費)
BOSS (蒙特卡羅模擬軟件)
CADPAC (劍橋量子化學計算軟件)(免費)
Car-Parrinello分子動力學(CPMD, ab-initio分子動力學計算軟件)(免費)
CHARMM (大分子分子力學模擬計算軟件)(部分免費)
Chem2Pac package (A computational Chemistry Integrator)(免費)
ChemTK Lite (QSAR軟件)(免費)
Chemweb計算化學在線工具：GAMESS(免費)
Clebsch-O-Matic (在線計算器)(免費)
Collaborative Computational Projects (協同計算計劃)
COLUMBUS (量化從頭計算分子電子結構程序集)(免費)
CrystalMaker Software (晶體結構可視化軟件)
DL_POLY (分子動力學模擬軟件)(免費)
DockVision (分子對接程序)(部分免費)
DPMTA (分子動力學並行模擬軟件)(免費)
Dr. Pablo Wessig 研究小組開發的計算化學軟件(免費)
eHiTS: Electronic High Throughput Screening
EMSL Gaussian Basis Set Order Form(免費)
GAMESS-UK (分子電子結構計算軟件)
GAMESS: The General Atomic and Molecular Electronic Structure System(免費)
Genebrowser (生物技術、基因治療資源導航)
Glide (分子對接程序)
GROMOS (通用分子動力學軟件包)(部分免費)
HyperChem (分子模擬)
Interprobe Chemical Services (分子模型化軟件)
Jmol (分子可視化軟件)(免費)
List of Computationally Sick Species (ab initio計算出現問題的物質、方法)
MacroModel (分子力學計算程序)
MARDIGRAS和CORMA (弛豫矩陣分析)(免費)
MCPRO (用於蛋白質和核酸的蒙特卡羅模擬軟件)
MDRANGE (分子動力學計算ion ranges)(免費)
MDynaMix (分子動力學計算軟件)(免費)
MidasPlus (分子建模軟件, 美國加利福尼亞大學舊金山分校計算機圖形實驗室開發)
MOE(分子模擬應用環境、方法開發平台)
MOLMOL (生物大分子3D結構分析和顯示、NMR結構解析)(免費)
MolPOV 2.0.8 (一個將PDB文件轉為POV-Ray文件的軟件)(免費)
MOLPRO 量子化學軟件包 (用量化從頭方法計算分子電子結構)(免費)
Mopac 2002 (通用半經驗量子力學程序)
NAMD (並行分子動力學計算軟件)(免費)
Norgwyn Montgomery (化學軟件公司)
NWChem (計算化學軟件包)
OpenEye (快速計算分子的靜電性質、形狀)
ORAC (用於模擬溶劑化生物分子的分子動力學計算程序, 意大利佛羅倫薩大學)(免費)
ORTEP-III (美國橡樹嶺國家實驗室晶體結構可視化--熱橢圓體繪圖程序)(免費)
OSIRIS Property Explorer (LogP, 溶解度、成藥可能性預測)(免費)
PAPA (計算粒狀物料的三維並行分子動力學計算程序)(免費)
PETRA (反應性參數預測，包括生成焓、鍵離解能等)(部分免費)
PharmTree (3D藥效團生成和化合物分類)
Pipeline Pilot (藥物發現集成平台)
PMDS (並行分子動力學模板庫)(免費)
PreADMET (ADMET預測)
Protein Domain Motion Analysis Software: DynDom （蛋白質分析軟件）(免費)
ProtoMol (分子動力學並行計算軟件)(免費)
PSI3量子化學軟件包(量化從頭計算)(免費)
Q-Chem (量子化學計算軟件包)
SGI應用於化學、生物信息學的軟件、硬件產品
SIGMA (分子動力學相關軟件)
SimBioSys (藥物設計軟件SPROUT)
SMILECAS 數據庫 (描述分子結構、子結構和復合結構的線性編碼系統)
SURFNET (量子化學計算程序)(免費)
Sweet (依據標準命名方法和分子順序建立糖類三維模型)
Swiss PDB Viewer (PDB蛋白質結構可視化軟件)
SYBYL/Base(分子模擬和藥物發現平台)
TINKER (分子設計軟件)(免費)
UCSF Chimera (可擴展的, 交互式分子圖形程序)(免費)
VAMP/VASP (採用從頭計算量子力學的分子力學)(免費)
VHMPT (螺旋膜蛋白拓撲結構顯示與編輯程序)(免費)
Virtual Molecular Dynamics Laboratory (分子動力學軟件)(免費)
voidoo(空腔探測軟件)(免費)
WAM: Web Antibody Modeling (抗體模型構建)(部分免費)
WebMO (基於3W界面的計算化學軟件包)(免費)
並行分子動力學模擬軟件DoD-TBMD(免費)
大分子對接程序Hex(免費)
大規模原子(分子)並行模擬器 LAMMPS(免費)
單晶和粉末衍射合作計算項目開發的免費軟件(CCP14)(免費)
蛋白質分子動力學模擬軟件：CONCOORD(免費)
蛋白質模擬資源導航，美國橡樹嶺國家實驗室ORNL
分子的物理化學性質在線計算 (用在基於結構的藥物設計, 可計算logP, PSA,等)(免費)
化合物3D結構VRML文件的自動生成(免費)
化學中的常用計算機軟件與資源(免費)
化學資源工具箱(免費)
計算機模擬的分子運動圖像集(DSMM)(免費)
可下載的教學軟件(倫敦大學瑪麗女王學院化學系提供)(免費)
量子化學網
美國華盛頓州立大學化學系：無機化學教學資源
美國加州大學聖地亞哥分校所開發的化學軟件 (化學反應計算、分子建模和可視化)
美國康奈爾大學理論中心計算生物服務單元提供的免費軟件 (計算生物與化學方面)(免費)
美國馬裡蘭大學：生物技術研究所Gilson研究小組
美國能源部Ames實驗室：經典分子動力學軟件AL_CMD(免費)
免費遠程計算：貴州大學GHPCC量子化學從頭計算系統(免費)
模擬蛋白質的並行分子動力學計算程序EGO(免費)
牛津大學：抗癌藥物分佈式計算項目 Screensaver Lifesaver
歐洲科學基金資助項目：分子模擬所面臨的挑戰 (Simu: Challenges in Molecular Simulations)
生物大分子結構分析和確認系列軟件(美國加州大學聖地亞哥分校大分子結構計算研究中心開發)(免費)
牙買加西印度大學Mona分校化學系所開發的免費軟件(免費)
應用於雙原子分子的數值Hartree-Fock程序(免費)
原子軌道3維模擬演示

海域對流層氣溶膠化學箱狀模型(MOCCA, 源代碼)

化工過程相關軟件
材料模擬計算算法庫MAP

Engineeringtalk (產品新聞)(免費)
GULP (General Utility Lattice Program)(免費)
過程(工程)相關的單位換算在線工具(免費)
化學工程進展CEP的化工軟件目錄(免費)
計算材料科學Mathub
綠色化學專家系統The Green Chemistry Expert System (GCES)
統計學數據集、軟件StatLib (archive of statistical datasets and software at Carnegie Mellon University)
製造業相關的軟件目錄(免費)

FEATFLOW 軟件(有限元方法計算和計算流體力學)(免費)
MARVIN'S PROGRAM (表面與界面模擬)(免費)
從Chemical Online查找最新發佈的化工軟件(免費)

3E Company (在線MSDS管理和信息服務商)
Actio Corporation (在線化學品管理解決方案提供商)
ANSYS CFD FLOTRAN使用指南(免費)
ANSYS Inc. Corporate (工程模擬軟件)
ANSYS使用手冊
AspenTech
Autodesk, Inc. (中國)
Autoplant plant design software
BARON (非凸性函數全局最優化問題求解)(免費)
CCSE Applications Suite(免費)
CFD(計算流體力學)的軟件, 數據, 視頻和文字資料 (美國愛荷華大學IIHR-水利科學與工程研究中心發佈)(部分免費)
CFDTutor and CFDExpert (CFD學習與模擬軟件)
ChemiSoft (化學工程相關軟件目錄)
ChemSage (無機物相圖計算)
ChemSep (多組分分離過程計算軟件)
Chemstations (過程模擬)
COADE, Inc. (管道應力分析與設計、壓力容器設計)
DESIGN II for Windows (過程模擬軟件)
DIPPR (物性數據)
DR Software, Inc. (MSDS管理軟件開發商)
Element DataSystem (環保實驗室信息管理系統)
Environmental Technology Network (與環境有關的過程軟件)
EPI Suite(與環境有關的物性估算程序包)(免費)
ePlantData (過程數據交換方法)
ESM Software(材料科學與工程軟件)
Flavor Selector 5.0 (調味劑管理工具)
Fluent Inc.(CFD軟件、流動和傳熱模擬)
General Algebraic Modeling System (GAMS, 數學規劃軟件
Haddock HazCom (MSDS專業服務公司)
HSE Systems (MSDS軟件開發以及管理服務商)
Hyprotech (過程模擬)
IDES
ImageTrak Software (MSDS管理軟件開發與服務)
ImageWave Corporation (MSDS管理數據庫和服務商)
InfoDyne Softwares (MSDS的建立與管理軟件, 針對歐洲標準)
LabView(儀器編程的圖形化編程環境軟件)
Logical Technology, Inc. (環境衛生和安全EH&S軟件和服務)
M-Base Company (物性數據庫和設計軟件)
MINOPT (模擬優化線性、非線性、混合整數、動態、混合整數非線性問題求解)
Modeling Fluid Flow using Smoothed Particle Hydrodynamics(免費)
Moldflow Corporation (注塑模擬)
MSDS Archive (將紙載體的MSDS文件轉換成符合OSHA標準的電子文檔)
MSDSpro (MSDS和化學品管理服務提供商)
MSDSystem (MSDS 管理, 搜索和修復軟件)
OLI Systems (水溶液系統的模擬計算)
Pacific Simulation (造紙過程模擬)
ParCFD Test Case
PenSim v2.0(青黴素發酵批處理過程模擬軟件，免費)
Philadelphia Mixers (攪拌器/混合器)
PHOENICS (流體力學計算軟件)
Prosim (過程模擬軟件)
Reaction Design (反應、物理汽相沉積PVD)
SafeTrax (MSDS創建工具)
Scandpower AS (石油業咨詢、過程模擬)
Selerant (配方產品管理工具, 技術數據表Technical Data Sheets, TDS創建工具)
SGI應用於化學、生物信息學的軟件、硬件產品
Sim42 (公開源代碼的化學過程模擬器項目)(免費)
Simons Technologies, Inc.
Simulation Sciences Inc. (SIMSCI)
Spotfire(決策支持軟件Spotfire DecisionSite)
Sunrise Systems (管道流動模擬)
SuperPro Designer (過程模擬)
Talos (MSDS 管理軟件)
THERIAK-DOMINO (平衡態及相圖計算)(免費)
Virtual Materials Group, Inc. (面向過程工程的熱力學應用產品開發)
WinSim Inc. (Windows、過程模擬軟件)
並行分子動力學模擬軟件DoD-TBMD(免費)
過程控制流程圖繪製與管理軟件ControlDraw 1(免費)
過程模擬環境ASCEND(免費)
韓國嶺南大學計算應用流體實驗室開發的免費CFD模擬軟件(免費)
化學反應動力學模擬JavaScript Kinetics Simulator(免費)
化學工程軟件目錄, www.cheresources.com
化學平衡計算程序EQS4WIN
揮發性有機物對大氣對流層影響的模擬(Tropospheric Chemistry Modelling)
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空氣和廢氣性質計算(Air and Exhaust Gas Properties V1.2)(免費)
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流體動力學模擬軟件包：FOAM
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水溶液反應庫及平衡計算Joint Expert Speciation Syetem (JESS)(免費)
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相圖計算軟件MTDATA
橡膠、塑料部件加工模擬(SIGMA Engineering)
意大利的裡雅斯特大學應用物理系DINMA分部開發的一些CFD軟件(免費)
英國工程領域高性能計算計劃CCP12 (High Performance Computing in Engineering, UK)
與過程工業相關的工程軟件導航 （荷蘭能源環境署）
與過程相關的小型計算工具, Process Associates of America

選對行業 站穩Ｍ型右段班

選對行業 站穩Ｍ型右段班
中時電子報 更新日期:2007/11/19 04:39 記者:本報訊

　「二○一○年時最熱門的工作，現在根本還不存在。」美國前教育部長萊禮（Richard Riley），面對新技術快速誕生，曾感嘆新興熱門行業的變遷，將會是學校最大的挑戰。


　根據美國暢銷書《寬頻新時代》的描述，現在每兩年新技術就成長一倍，到二○一○年時，每七十二小時即會增加一倍。


　產業結構跟著新技術前進，不斷變遷，失去競爭力的黃昏產業逐漸沒落，企業關門倒閉後，員工飯碗也跟著不保；反觀新興行業趁勢而起，迅速發展茁壯，旗下員工獲得的回饋自然水漲船高。


　六、七年級生雖無法預知十年後的熱門行業，但只要下功夫多搜集資訊，仍有蛛絲馬跡可以探知一二。


　根據勞委會職訓局委託一一一一人力銀行調查，綜合全球五百大熱門職缺、政府二○一八年發展計畫等國內外產業與職場發展趨勢後，交叉比對出台灣九大最具前景的熱門行業：觀光休閒、電信服務、醫療健康服務、個人服務、生技美容、無線寬頻、顧問服務、保全服務，以及殯葬禮儀師等其他行業。


　負責這項調查的一一一一人力銀行執行長金仁說，有些熱門行業如觀光休閒業、醫療健康服務業存在已久，但是受到國內財富分配、人口結構等主客觀因素的改變，增添許多不同元素後，價值獲得提升，進而衍生出如地方產業行銷輔導師、國際醫療規劃師等新興職業。


　政大勞研所教授成之約指出，很多年輕人就讀的科系不符合巿場需求，不妨找尋有發展前景、自己不排斥的職業，即使因為所學不符而影響起薪、職位，但只要肯學習、努力，未來仍可望躋身Ｍ型社會的右段班。